Showing posts with label Mapping. Show all posts
Showing posts with label Mapping. Show all posts

Saturday, 4 June 2022

Searching for Fort Caroline.

On 22 June 1564 a group of predominantly Hugenot French settlers founded the colony of Fort Caroline on a waterway they identified as the 'River of May' in French Florida, under the leadership of René Goulaine de Laudonnière. The colony is thought to have been the first fortified European settlement in North America, but lasted for 15 months before being attacked and captured by a Spanish force led by Pedro Menendez on 20 September 1565. Following the attack the French survivors were taken to a beach called 'Matanzas' ('slaughter'), where the men were killed one at a time, before the women and children were loaded onto ships and taken to Havana, their subsequent fate being unknown. 

The fort was subsequently renamed Fort San Mateo, and occupied by a Spanish military force. On 25 April 1568 the fort was attacked by a force of French corsairs led by Dominique de Gourgues, who overwhelmed the Spanish force, before hanging all captured Spaniards and dumping the fort's cannons into the river. The site was briefly re-occupied by the Spanish, but abandoned in 1580 amid deteriorating relations with the local Native American population.

The site of Fort Caroline has subsequently been lost, but is considered to be an important location in American history, as its founding predated the foundation of the Lost Colony of Roanoke in modern Virginia by 21 years, the foundation of the Jamestown Fort by 45 years, and the arrival of the Pilgrims in Massachusetts by 56 years. As such the location of Fort Caroline has been the subject of a large amount of speculation over the past century, with several locations proposed, the most popular of which is on the St Johns River, to the north of St Augustine, where the  Fort Caroline National Memorial is located.

In a paper published in the Journal of Historical Archaeology and Anthropological Sciences on 4 March 2022, Anita Spring of the Department of Anthropology at the University of Florida and Fletcher Crowe of Bethune-Cookman University re-examine the evidence for the location of Fort Caroline, and conclude that it should in fact be searched for on the St Mary's River, rather than the St Johns.

Drawing of Fort Caroline Attributed to Jacques Le Moyne and published by Théodor De Bry in 1591. Spring & Crowe (2022).

Spring and Crowe examined a collection of sixteenth century French and Spanish manuscripts relating to the site, including the accounts of René Goulaine de Laudonnière and Dominique de Gourgues, and identified 31 geographical criteria which could be used to identify the site of Fort Caroline in these documents, and used them to create a matrix against which the St Johns River and St Mary's River locations could be compared. 

Most of these criteria could be applied to both the St Mary's River and the lower part of the St Johns River, from its mouth to Blount Island where the river turns sharply to the south, although the St Johns River lacks a number of features described in the historic documents, notably two islands at the mouth of the river and parallel freshwater and saline channels. Furthermore the documents describe the river as deep and fast flowing, which is true of the St Mary's River but not of the St Johns.

As well as the written accounts made by eyewitnesses to the events, Spring and Crowe examined a series of maps of the area, made by French and English cartographers between the sixteenth and early eighteenth centuries.

The first of these maps was made by the French explorer Jean Ribault in 1562, whilst scouting for a site for the future colony at the behest of Nicolas Barré (known as 'Parreus'). This map shows the mouth of a river immediately west of the first island north of the River of May. Based upon Spring and Crowe's calculation that the River of May is the modern St Mary's River, this island would be Cumberland Island.

Parreus Map of French Florida, 1563. Shows a river west of the first island north of the River of May. If the River of May is the St. Marys River, this island is Cumberland Island, and the map is correct. Spring & Crowe (2022).

Modern map of the same area. Google Maps.

The second map examined was made by the English cartographer John White in 1587. White served as the governor of the second (failed) attempt at founding a colony at Roanoke in modern Virginia from 1587, and is known to have consulted with the French artist and cartographer Jacques Le Moyne, who took part in Jean Ribault's expedition to the area. This map shows a River des Daufins to the south of the River of May, which Spring and Crowe identify as the St Johns River.

Detail of Southern Portion of Map of North America by John White, 1587. Note that the 'River des Daufins' with its sharp bend to the south, is clearly the St. Johns River. Spring & Crowe (2022).

Finally Spring and Crowe looked at a map made by French cartographer Jacques Nicolas Bellin in 1744. This map identifies the St Mary's River as the San Mateo, the name used for it by the Spanish when they ruled the area, and shows a point to the west of the mouth of this river labelled 'Ici… la Caroline' ('Here... the Caroline'), which presumably refers to the location of Fort Caroline. This map also identifies the St Johns River as the St Augustine River (again a name known to have been used by the Spanish for this river), with a note next to it indicating that it was formerly known as the formerly known as the River of Dolphins, strongly supporting the idea that the three names refer to the same waterway.

Detail of Southern Portion of Map of French Florida by Jacques Nicolas Bellin (1744. The French knew the River of Dolphins as the Seloy River. The map clearly shows Fort Caroline well north of the St. Johns River. Spring & Crowe (2022).

The Spanish assault of 1565 is known to have involved 500 men marching north from a place called 'Seloy' to attack Fort Caroline. Traditionally, 'Seloy' has been associated with the city of St Augustine, which is thought to be the oldest continuously occupied site in North America, and from which it would be possible to march north to the St Johns River without crossing any other body of water.

This would involve marching a distance of 35 miles, in four days, amid what witnesses described as driving rain, something possible, but highly implausible for a sixteenth century armed force of this size. 

French reports at the time record that the Spanish fleet disembarked the military force 8-10 leagues to the south of Fort Caroline, which, assuming a sixteenth century French league is 2.2-2.3 miles, would imply a distance of about 20 miles, which is a more reasonable achievement. This is also the approximate distance between the St Johns and St Mary's rivers, suggesting that Menendez could have landed his troops on the St Johns River before marching north to fight the French.

In 2014-15 and 2017 the Fort Caroline Archaeology Project carried out a series of excavations at four different locations on the St Mary's River, recovering over 100 artifacts. They also examined collections of objects gathered by local residents, and carried out surveys of the St Mary's River bottom, which revealed a number of items of interest, including stone markers, ballast stones, small clay objects, glass bottles of later periods, and a large stone block with a hole that possibly could be part of a French oven, all of which were deposited with the Florida Museum of Natural History. A fragment of wooden artifact collected close to a spring which might have provided the colony with fresh water yielded a carbon¹⁴ date of 1530-1600 years.

A Native American burial mound close to the St Mary's River, which was excavated by privately contracted archaeologists is known to have yielded a French halberd of a type that Dominique de Gourgues is known to have given to local warriors who took part in his attack on the Spanish-held Fort Caroline, as well as a number of other European artifacts, including an iron knife and several glass beads.

From this evidence Spring and Crowe deduce that the current available evidence strongly supports a position on the St Mary's River for Fort Caroline, and that, as late as the mid-eighteenth century, geographers and historians appear to have taken this location for granted, with the now-popular hypothesis of a location on the St Johns River apparently being a modern fallacy. 

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Wednesday, 1 September 2021

Estimating the risks presented by radon gas from geological sources in Perak State, Malaysia.

Radon is a naturally occurring radioactive noble gas produced as part of the decay chain of the readionuclides uranium²³⁸, thorium²³³, and uranium²³⁵. The most abundant isotope of radon is radon²²², which is a part of the uranium²³⁸ decay chain, which leads eventually to lead²⁰⁶, although there are several further stages in the decay chain between radon²²² and lead²⁰⁶, all of which are reactive and radioactive heavy metals. Radon²²² is naturally given off by many granitic rocks, and unlike most other radionuclides, can be easily inhaled, making it responsible for about 50% of all Human exposure to ionising radiation globally, and the leading cause of lung cancer after smoking internationally, according to the International Agency for Research on Cancer, with prolonged exposure to even relatively low levels of the gas presenting potential health problems. Radon is particularly prone to accumulating in buildings built upon rocks or soil which emit the gas, which makes assessment of the risks presented by radon an important part of the planning process in areas where it can be a problem.

There are essentially two ways to assess the risks presented by radon in any given area; either measure the accumulation of the gas within existing buildings, or assess the dangers presented by the local geology. The latter method is generally preferable, and may be done directly measuring radon gas in the soil, by measuring gamma radiation in the area, or by measuring the uranium and/or radon levels in rocks and soils remotely during aerial surveys.

The potential of a soil or geological formation to release radon into the environment is known as its Geogenic Radon Potential, which is often used to assess the risks of radon accumulating within buildings, although sometimes a combination of radon activity concentration and soil permeability is used to construct hazard maps.

Relatively few measurements of radon in soil in Malaysia have been undertaken, although those that have produced readings as high as 375.42 kBq/m³ (readings of above 300 375.42 kBq/m³ are generally considered harmful). No data appears to have been collected on the hazards presented by radon in Perak State on Peninsula Malaysia, despite the presence of extensive granite outcrops, considered to present the highest geologic risk of radon release.

In a paper published in the journal PLoS One on 28 July 2021, Habila Nuhu of the Department of Physics at Universiti Teknologi Malaysia and the Department of Science at Plateau State Polytechnic, Suhairul Hashim also of the Department of Physics, and of the Ibnu Sina Institute for Scientific and Industrial Research at Universiti Teknologi Malaysia, Muneer Aziz Saleh of the Nuclear Engineering Programme at Universiti Teknologi Malaysia, Mohamad Syazwan Mohd Sanusi, again of the Department of Physics at Universiti Teknologi Malaysia, Ahmad Hussein Alomari of the Energy and Minerals Regulatory Commission in Amman, Jordan, and Mohamad Hidayat Jamal, Rini Asnida Abdulla, and Sitti Asmah Hassan, of the Faculty of Engineering at the Universiti Teknologi Malaysia, present the results of a field study of radon activity concentration and soil permeability in Perak State, Malaysia, undertaken with a view to creating a Geogenic Radon Potential map of the state, which should be of use to future planners.

Perak province is located in the northwest of Penninsula Malaysia. The peninsula is made up of two tectonic blocks, the Sibumasu Block to the west and the Sukhotai Arc (or Eastern Malaya Block) to the east. The two blocks are separated by the Bentong-Raub Suture Zone, which formed when they converged in the Triassic, to form part of the core of the Sundaland Continental Block, which comprises much of modern Southeast Asia. Much of the Sibumasu Block is covered by Peninsula Malaysia's Main Granite Range. The area is divided into four different geological regions, Quaternary succession of continental and shallow marine sediments, a Triassic-Jurassic succession of deeper marine sediments with volcanic tuff (ash) beds, a Silurian succession of sediments and metamorphic rocks, and a suite of intrusive rocks, mainly granite. Location sites for sampling were chosen at random across the state, but attempting to include each major rock and soil type; private land or land where permits were needed to carry out investigative work were also excluded. At each test site the local geology was recorded, as was any previous sampling work by other researchers. A total of 70 sites were visited.

 
Geological map of Perak state. Nuhu et al. (2021).

Nuhu et al. detected radon activity concentrations of between 0.11 and 434.5 kBq/m³ at localities across Perak State, with an average reading of 18.96 kBq/m³. The majority of the readings (81%) were low (defined as below 20 kBq/m³), while 13% were high (between 20 and 50 kBq/m³) and 6% very high (more than 50 kBq/m³). Soils derived from granite rocks, and young aluvial (river) sediments (which probably also contained material derived from granites, were found to have elevated radon activity, with average radon activity concentration values of between 4.28 and 44.48 kBq/m³. The highest value recorded in the study, of 434.5 kBq/m³, was obtained from the most western granitic region of the state. Since radon is associated with granite rock, these findings were in line with predictions. Moderately high readings were also associated with soils from mined and urban areas, as well as soils derived from sedimentary rocks. In these areas radon activity concentration values ranged from 8.48 to 9.62 kBq/m³. The lowest values were obtained from soils derived from marine sources on the coastal plains. Here the highest reading was 27.6 kBq/m³.

 
Map of radon activity concentration in soil gas Perak state. Nuhu et al. (2021).

Both soils derived from Quaternary sediments and those from Silurian rocks had average radon activity concentration values below the overall for the province, with Quaternary rock-derived soils producing an average reading of 1.13 kBq/m³, and Silurian rock-derived soils producing an average reading of 1.4 kBq/m³. Soils derived from the Triassic-Jurassic rock sequence were far closer to the average for the state, with an average reading of 1.97 kBq/m³ from Triassic-Jurassic rock-derived soils and an average of 1.98 kBq/m³ for the state as a whole. Readings in these soils ranged from 1.0 to 106.5 kBq/m³. Readings from areas with intrusive igneous rocks were the highest, ranging from 9.81 to 434.5 kBq/m³.

 
Box plot of radon activity concentration in geological formations of Perak state. Nuhu et al. (2021).

The release of radon gas into the environment is also partially controlled by soil permeability, with higher permeability soils allowing more easily the upward migration of the gas. Nuhu et al. divided soils into three classes (High, Medium, and Low). Soils derived from Silurian and Quaternary sources tended to have the lowest permeability, with those of Triassic-Jurassic rock-derived soils being intermediate, and the highest permeability being found in rocks derived from granites. Geographically, the least permiable soils were found on the coastal plains of the west of the state, median values were found in the northern, central, and southern areas, and the most permeable soils were found in the eastern part of the state, where the rocks are primarily granitic.

 
Soil permeability map of Perak state. Nuhu et al. (2021).

Finally, Nuhu et al. calculated the geogenic radon potential for each area of the state, by combining the data on radon production and soil permsability, dividing the state into low-, medium-, and high-risk areas. This tended to follow the local geology, with high risk zones primarily occurring in areas with granitic bedrocks, medium risk zones in areas with Triassic-Jurassic bedrocks, and low risk zones found in areas with Silurian or Quaternary bedrocks.

 
Geogenic radon potential map of Perak state Malaysia. Nuhu et al. (2021).

Nuhu et al. produced a number of maps outlining the risks presented by geogenic radon gas in Perak State, Malaysia. The highest risks were found to be in the central and eastern parts of the state, where soils tend to be derived from intrusive granitic rocks, with the lowest risks being found in the southeast and north. However, this is not an absolute rule, and there are areas with higher risks than would be predicted by simply extrapolating from the geology, and it is possible that other higher risk pockets exist undetected in the areas classified by Nuhu er al. as low risk. These maps produced are intended be useful as a base for authorities monitoring radon control and mitigation, in dwellings and workplaces.

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Tuesday, 2 March 2021

International Union for Conservation of Nature publishes a comprehensive system for classifying all ecosystems.

The International Union for Conservation of Nature has published a Global Typology of Ecosystems, the first-ever comprehensive system for classifying and mapping all ecosystems on Earth based on both their functions and composition. The typology allows for more coordinated and effective approaches to conservation management, according to a press release issued on 1 March 2021.

'Many of the world’s ecosystems are under acute risk of collapse, with grave consequences for the survival of species, genetic diversity, ecosystem services and Human wellbeing. To sustain them, it’s critically important that the post-2020 Global Biodiversity Framework contains explicit, ambitious goals for the conservation of ecosystems alongside species,' said International Union for Conservation of Nature Director General Bruno Oberle. 'This first standardised, spatially explicit ecosystem typology provides the infrastructure that is needed to set and track such goals.' 

 
Rocky shore, Seilebost, Isle of Harris, Scotland. Helen Hoston/Alamy Stock Photo/IUCN Global Ecosystem Typology.

The typology defines the key biophysical features of 108 major ecosystem types throughout the oceans, freshwater and land, and describes the processes that sustain them as well as their global distributions. It encompasses ecosystems that are shaped by Humans, such as croplands and dams, as well as vast forest wilderness, deserts, deep ocean trenches, and even ecosystems buried below ground and beneath ice sheets. This systematic approach to classifying ecosystems will help identify which types of forests, reefs and wetlands, for example, are most critical to biodiversity conservation and the supply of ecosystem services, and which are at greatest risk of collapse.

'By grouping similar ecosystems according to their characteristics and functions, this new typology reveals patterns that might otherwise remain hidden. It will allow us to recognise similarities between related ecosystems and to apply what we learn about sustainable management of estuaries in China, for example, to similar estuaries in Nigeria,' said the typology’s lead author, David Keith, of the Centre for Ecosystem Science of the University of New South Wales in Sydney and member of the International Union for Conservation of Nature's Commission on Ecosystem Management. 'Understanding the common risks that similar ecosystems face ultimately helps to develop ways to protect them.'

 
Mirror lakes at the head of Milford Sound, New Zealand. Christopher Meder/IUCN Global Ecosystem Typology.

In addition to enabling the setting and tracking of global biodiversity conservation goals, the new framework will inform the Red List of Ecosystems, the International Union for Conservation of Nature’s standard for measuring risks of collapse faced by the world’s ecosystems. It will also provide a solid foundation for the System of Environmental-Economic Accounting, an ongoing initiative by the United Nations to measure the contribution of the environment to the economy through so-called ecosystem services, and the impact of the economy on the environment.

'This work fills a knowledge gap that was hindering our ability to measure progress on the sustainable management of the world’s ecosystems. It’s a very timely breakthrough, as the world is developing new global policy initiatives that will be critical for a sustainable future, including the post-2020 framework for the conservation of ecosystems and species under the United Nations Convention on Biological Diversity,' said Angela Andrade, Chair of the International Union for Conservation of Nature’s Commission on Ecosystem Management.

 
Masoala National Park, Madagascar. Frank Vassen/IUCN Global Ecosystem Typology.

In addition to the publication, the International Union for Conservation of Nature has also launched a fully interactive website, introducing the typology and enabling users to explore the diversity of the world’s ecosystems.

'The website’s mapping function allows users to see where on the planet different ecosystem types exist, and to explore their functions and the biodiversity that depends on them,' said Richard Kingsford, Director of the Centre for Ecosystem Science at the University of New South Wales, and a member of the research team that developed the typology.

The typology was developed by more than 100 ecosystem scientists representing the International Union for Conservation of Nature's Commission on Ecosystem Management and 85 scientific institutions, led by the University of New South Wales, Arizona State University and King's College London of the PLuS Alliance and Deakin University.

 
Petworth, Sussex, England. David Keith/IUCN Global Ecosystem Typology.

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Wednesday, 29 April 2020

Emiliania huxleyi: Modelling how an Atlantic Coccolithophore is invading the Arctic Ocean.

The European Arctic Corridor is the main gateway to the Arctic Ocean, where 80% of both in- and outflow takes place. One of the most prominent feature of the European Arctic Corridor is the northward flowing North Atlantic Waters entering the Arctic Ocean through two main branches, which separate around 70°N. One branch keeps flowing northward toward Fram Strait while the second one turns eastward into the Barents Sea. Over the last three decades, in a context of amplified warming and sea-ice loss, substantial changes have been documented in the North Atlantic Water inflow with a twofold increase of its volume occupation and a northward shift of the polar front structure in the Barents Sea. The North Atlantic Water inflow largely controls the physical and sea-ice conditions of the region In addition, almost 50% of the total Arctic primary production takes place in the European Arctic Corridor, which is of major importance for fisheries. Recent warming of the European Arctic Corridor related to the North Atlantic Water inflow has been suspected to trigger poleward intrusions of temperate phytoplankton and species from higher trophic levels. By carrying biomass and nutrients produced elsewhere, bioadvection has recently been proposed as an 'essential mechanism' for ecosystem dynamics in the Arctic Ocean. Although the actual role of advection has already been identified as a potential driver altering zooplankton dynamics, it has never been assessed quantitatively from observations for phytoplankton in the European Arctic Corridor, or more generally in the Arctic Ocean.

In a paper published in the journal Nature Communications on 10 April 2020, Laurent Oziel of the Ocean and Ecosystem Sciences Division at Fisheries and Oceans Canada, the joint Takuvik International Research Laboratory of Université Laval and the Centre National de la Recherche Scientifique, and the Laboratoire d’Océanographie de Villefranche-sur-Mer of Sorbonne Université, Alberto Baudena, also of the Laboratoire d’Océanographie de Villefranche-sur-Mer, Mathieu Ardyna also of the Laboratoire d’Océanographie de Villefranche-sur-Mer, and of the Department of Earth System Science at Stanford University, Philippe Massicotte and Achim Randelhoff, also of the Takuvik International Research Laboratory, Jean-Baptiste Sallée, again of Sorbonne Université, Randi Ingvaldsen of the Institute of Marine Research, Emmanuel Devred, also of the Ocean and Ecosystem Sciences Division at Fisheries and Oceans Canada, and Marcel Babin, again of the Takuvik International Research Laboratory, present the results of an investigation into how ocean currents control the spatial dynamics of a specific Coccolithophore bloom-forming species, Emiliania huxleyi.  

The European Arctic Corridor. Bathymetry and surface circulation. The Atlantic currents are in red, the Arctic or Polar Waters are in blue and the Coastal Waters are in green. The southern Barents Sea Polar Front is illustrated in black dashed line and separates the Atlantic Waters from the colder and fresher waters from the North. Oziel et al. (2020).

Emiliania huxleyi is usually associated with the surface layer of the temperate North Atlantic Waters in summer, typically in a post-spring bloom context characterized by low nutrients, low light and strong stratification. Since Emiliania huxleyi does not form winter resting spores, this tracer of Atlantic ecosystem is generally considered to be a summer visitor in the Barents Sea, unlike neritic Diatoms species. A combination of bottom-up (i.e. winter darkness, cold temperatures and intense vertical mixing) and top-down controls (i.e. zooplankton grazing, viral lysis) prevent Emiliania huxleyi from year-to-year survival in the north-easternmost parts of the Barents Sea. Because of their high abundance in Emiliania huxleyi (115 000 000 cells per litre), coastal regions and fjords of the Norwegian Sea have been suspected to be the source of Emiliania huxleyi for the whole European Arctic Corridor.

Using a Lagrangian tracking approach based on satellite derived current fields, Oziel et al. explored how the advection of Emiliania huxleyi cells from these upstream coastal temperate regions shapes the distribution of the massive Emiliania huxleyi blooms in the Barents Sea (via the 'seeding effect'). By combining satellite-derived altimetry with ocean-color Particulate Inorganic Carbon (a Coccolithophore biomass proxy) estimates, Oziel et al. demonstrate a major role of bio-advection in phytoplankton transport along the European Arctic Corridor.

An individual Emiliania huxleyi cell. Stig Haugen/Institute of Marine Research.

To document the interannual and decadal variability of surface North Atlantic Water currents, Oziel et al. first performed an statistical analysis of Sea Level Anomalies from 1993 to 2016, on which the seasonal signal was removed. The analysis showed that the two variables accounted for more than 80% of the non-seasonal variability. A dipole structure emerged, centered on the North Atlantic Waters path between the Barents and Norwegian Sea shelves (east of 5°E) and the center of the Norwegian Sea (west of 5°E). The associated time-series showed a linear positive trend over the last 24 years with high energy at the interannual and decadal time scale. This trend toward a more positive phase corresponds to an increase of the sea level gradient across the North Atlantic Waters path, hence intensifying North Atlantic Waters currents, while negative phases are associated with weaker North Atlantic Waters currents.

Statistical analysis of Monthly averaged Sea Level Anomalies in the European Arctic Corridor. The sum of the first two modes account for more than 80% of the total variability. Oziel et al. (2020).

To reveal the impact of changing sea level on surface velocity fields, absolute surface geostrophic velocities, derived from Absolute Dynamic Topography fields were mapped during the extreme negative (1993) and positive (2015) phases of the analysis. These two contrasting years illustrate the ongoing strengthening of the ocean surface circulation in the European Arctic Corridor associated with the Atlantic inflow. Surface geostrophic current linear trends showed that surface currents changed in most of the Atlantic pathway In the Norwegian Sea, the increase in the Atlantic surface current speed reached 2 mm per second per year, corresponding to a relative increase ranging from 30% on the shelf to 100% in the basin. The surface currents in the eastern Barents Sea-Atlantic corridor also significantly increased by about 6 mm per second per year, an increase in flow rate of about 14%. The positive phase associated with stronger north-eastward North Atlantic Waters surface currents since year 2000 reflects an increase in advection at or near the surface. This result is consistent with the recent trends in North Atlantic Waters current velocities observed upstream in the Nordic Seas or modelled in the Barents Sea.

Surface absolute geostrophic velocities during the extremums of the timeseries which are, respectively, reached in (a) December 1993 (minimum) and (b) 2015 (maximum) with (c|) the corresponding absolute linear trend of the entire time-series (all months) over the 1993–2016 period. Areas covered by sea ice (sea-ice concentration over 15%) or with insufficient data coverage for the trend (less than 50%) are in dark gray. Oziel et al. (2020).

The interannual fluctuations as well as the long-term trend observed in the time-series of surface geostrophic velocities are mainly attributed to the dynamics of the North Atlantic Subpolar Gyre, and to the atmospheric forcing of the North Atlantic Oscillation, which are both tightly coupled. This suggests that the increase in surface advection in the European Arctic Corridor is likely due to a natural multidecadal oscillation related to the upstream synoptic oceanic circulation and atmospheric forcing, which could, in turn, drive long-term climatic change in the Barents Sea.

The first hypothesis that ocean currents control the summer spatial distribution of Emiliania huxleyi in the Barents Sea was tested using a Lagrangian model. Oziel et al. advected virtual particles (considered as the inoculum of Emiliania huxleyi cells), using observations of surface geostrophic velocities, from their expected overwintering location in March (defined by sea surface temperatures greater than 4°C and distance from coast no more than 180 km). This model revealed that the spatial distribution of the virtual particles at the end of the advection period matched the extent of Emiliania huxleyi blooms (evidenced by satellite-derived Particulate Inorganic Concentration), with 80% of tracked particles ending up within 50 km of an Emiliania huxleyi blooming location. The year-to-year robustness of the matchup between virtual particles and Particulate Inorganic Concentration clearly supports the fact that the North Atlantic Waters surface currents shape the location and extent of Emiliania huxleyi blooms in the European Arctic Corridor.

Poleward expansion of Emiliania huxleyi (EHux) in the European Arctic Corridor. Comparison between 1998 (a) and 2015 (b). The initialisation (inoculum) of virtual particles in March are illustrated by brown dots. During 6 months, particles drift with the Norwegian Atlantic Current (red arrows) as the ocean seasonally warms as illustrated by the northward expansion of the 4 °C isotherm. In August, the particles end up in positions indicated by the red dots. In the background, remotely sensed Particulate Inorganic Concentration indicating Coccolithophore biomass in summer (July–August–September) is shown in blue colors. Areas with no data are in dark gray. Oziel et al. (2020).

It is noteworthy that the particles reached further north and east in the European Arctic Corridor in 2015 than in 1998, in agreement with Emiliania huxleyi blooms. The north-eastward expansion of the Emiliania huxleyi bloom, expressed here as the distance reached by the leading-edge increased on average by 325 km during the last 19 years as indicated by ocean-color observations, in close agreement with previous estimations (324 km, 40–50°E, 1989–2016) and with the estimates from Oziel et al.'s model.

The 4 °C surface isotherm is considered for Emiliania huxleyi as the lowest temperature required for sufficient growth to allow bloom formation. However, the Emiliania huxleyi blooms do not seem to follow this isotherm in summer and appear to be constrained by another factor. For example, the north-eastward expansion of the winter 4°C isotherm, which delimits the areal extent of the inoculum in Oziel et al.'s model, could contribute to reduce the distance between the Emiliania huxleyi winter location and the Arctic domain. To test this hypothesis, Oziel et al created two additional models to examine both the role of currents and winter temperature on the poleward expansion of Emiliania huxleyi. In the second model Oziel et al. constantly initialised the virtual particles at the same inoculation region for all years, using a climatological mean temperature field to determine the inoculation region. Hence, the second model exclusively reflected the role of currents on the interannual variability of the advected particles. In contrast, in the third model, the constant inoculation region varied from one year to another, but Oziel et al used a climatological mean current to advect the particles. In this way, the interannual variability of the advected particles due to interannual variability of the inoculation region was quantified. The interannual Particulate Inorganic Concentration leading-edge location was highly correlated with the leading-edge from the second model, suggesting a stronger control of the bloom expansion by currents than by winter temperature. On the decadal scale, currents were found responsible for the 56% (240 km) increase in the long-term leading-edge expansion against 44% (186 km) for winter temperature, when compared to the first model. This significant increasing trend in current velocities was also revealed by the greater distance covered by the virtual particles reaching the Barents Sea, which increased by 110 km on average since 1993.

Shifting position of the leading-edge Emiliania huxleyi bloom distribution. Shifting position from ocean-colour Particulate Inorganic Concentration (a), and the three models (b)–(d) for the last 19-years (1998–2016). The comparison between the first model (EXP1), (b) with the second (EXP2), (c) and the third (EXP3), (d) aims at estimating the relative contribution of currents (EXP2, constant temperature) vs. temperature (EXP3, constant currents) on the total Emiliania huxleyi poleward expansion (EXP1, varying temperature and currents). The right panel is a schematic illustration of the poleward expansion of the Emiliania huxleyi with the winter 4°C isotherm (lowest temperature for a ‘regular’ Emiliania huxleyi growth) in blue and the summer bloom position (northern boundary) in red. The two extreme years 1998 (dashed) and 2015 (solid) are represented. Arrows indicate the contribution from temperature and/or currents keeping the same color code. Oziel et al. (2020).

Increasing water temperature has previously been assumed to be the main driver of the spatial distribution of Emiliania huxleyi blooms in the Barents Sea. Oziel et al.'s results demonstrate that the primary driver of the Emiliania huxleyi dynamics (i.e., spatial distribution and timing) could be, in fact, stronger surface currents, which in turn intrinsically shape the temperature field and frontal structures. Oziel et al. show that oceanic currents (i.e. their intensity and fluctuations) drive the spatial distribution of the bloom, its interannual variability and more than 50% of the long-term poleward expansion of Emiliania huxleyi bloom in the Barents Sea. More importantly, from 2006 and onward, the contribution of water temperature to the expansion of Emiliania huxleyi blooms becomes negligible, and its poleward expansion is entirely due to the accelerating currents.

Emiliania huxleyi is largely studied for its significant role in marine geochemical cycles, as illustrated by its sensitivity to ocean acidification, its effect on carbon dioxide pressure and carbon dioxide uptake, and its role on carbon export by providing calcite ballast effect. In Oziel et al.'s study Emiliania huxleyi was used as an indicator of Atlantic ecosystems. By expanding poleward and doubling its areal extent in the Barents Sea, Emiliania huxleyi attests to the ongoing 'Atlantification' of the Arctic Ocean. Both arctic and Atlantic domains have distinct ecological signatures, and the latter is undeniably 'invading' the former. Advected with the surface currents, Emiliania huxleyi will have to survive during the travel (for example avoiding grazing by zooplankton, and subduction under the polar mixed layer in the Fram Strait) until finding more favourable blooming conditions in the Barents Sea in summer. The fate of Emiliania huxleyi in the Barents Sea is therefore of major importance as it determines the potential 'seeding effect' of Emiliania huxleyi in the Arctic regions. Emiliania huxleyi seems to be adapted to the low light, low nutrient, oligotrophic and highly stratified conditions of the North Atlantic Waters in summer such that its expansion, growth and blooming in the Arctic Ocean will be limited at some point by those constraints (bottom-up) but also by the grazing pressure (top-down).

Despite its adaptation to low light conditions, Emiliania huxleyi still requires sufficient light levels to sustain the energy-demanding calcification of its coccoliths. Such conditions are met in highly stratified oceans where Emiliania huxleyi can accumulate in the surface layer. At high latitudes (more than 81°N), even with sea surface temperature above 3 or 4 °C, the survival of Emiliania huxleyi would require adaptation to rapidly decreasing solar radiations in late summer. Emiliania huxleyi's fate thus mainly relies on its ability to drift, with the appropriate timing, to highly stratified and temperate areas that allow it to stay in the surface euphotic layer. These conditions would likely be met in the Eurasian interior shelves of the Arctic Ocean (i.e. the Kara, Laptev, and Siberian seas) where surface waters are warming and freshening. If the increase in advection along the shelf slope continues in the future, Oziel et al. expect Emiliania huxleyi to become a summer resident of the newly 'Atlantified; Eurasian interior shelves, as previously revealed during the last interglacial.

By driving such a poleward expansion, advective processes could affect the entire marine ecosystems by shifting species distribution and modifying interactions at higher trophic levels. The concomitant decline of silicate concentrations in North Atlantic Waters may also contribute to the success of non-silicifying and small phytoplankton such as Emiliania huxleyi. n addition, a change toward temperate pelagic species could have an impact on energy transfer to higher trophic levels, including Marine Mammals and commercial Fish stocks. Considering the role of 'bio-advection' in ecological models (i.e., trait-based and niche-based approaches) must improve predictions of community shifts. The comparable increase in poleward advection of Pacific waters occurring in the Bering Strait suggests that the shrinking polar domain of the Arctic Ocean may be prone to intrusions of temperate species at a pan-Arctic scale.

See also...

https://sciencythoughts.blogspot.com/2020/04/looking-for-causes-of-recurring.htmlhttps://sciencythoughts.blogspot.com/2020/04/using-high-throughput-sequencing-to.html
https://sciencythoughts.blogspot.com/2018/11/glacial-flour-creates-dust-storm-in.htmlhttps://sciencythoughts.blogspot.com/2017/10/algal-bloom-covers-much-of-western-lake.html
https://sciencythoughts.blogspot.com/2015/03/methyl-mercury-levels-in-feathers-of.htmlhttps://sciencythoughts.blogspot.com/2014/03/a-new-species-of-golden-algae-from.html









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Tuesday, 28 April 2020

Utilising undergraduate research to hunt for gold-precipitating Bacterial lineages.

The potential benefits from the study of the unique abilities of Bacteria to everyday Human life is ever more obvious. Bacteria are used industrially in food preparation, drug production, waste treatment and many other roles. Advances in biotechnology techniques have facilitated the use of known Bacterial species and their enzymes, proteins and pathways. For example, it is now possible, and indeed not very difficult, to identify genes of interest in a bacterial species, clip those genes out of that species and insert them into another work horse species of Bacteria to allow the products of those genes to be produced industrially. Ironically, as our ability to harness the power of Bacteria becomes ever more sophisticated, one of the key challenges is still finding the useful Bacteria in the first place. In a world with as many as a trillion Bacterial species, how does one speed the discovery of Bacterial species with a particular use or even simply strains of a particular bacterial taxon with sequences of interest? One approach is to engage citizen scientists. In as much as the first step in the discovery of novel, useful microbes is often collection from nature, collections made by the public have the potential to speed up this key and often rate-limiting first step. What is more, in a rapidly interconnected digital era, the potential for truly global projects that rely on hundreds, thousands, or even hundreds of thousands of individuals is ever greater.

In a paper published in the journal PeerJ on 14 April 2020, Noah Riley of the Department of Biological Sciences at North Carolina State University, Carlos Goller, also of the Department of Biological Sciences and of the Biotechnology Program at North Carolina State University, Zakiya Leggett of the Department of Forestry and Environmental Resources at North Carolina State University, Danica Lewis and Karen Ciccone of North Carolina State University Libraries, and Robert Dunn of the Department of Applied Ecology at North Carolina State University, the Natural History Museum of Denmark at the University of Copenhagen, and the German Centre for Integrative Biodiversity Research, describe the results of a study using a citizen science approach to to detect new species of the gold-precipitating Bacterium Delftia, on a university campus.

Citizen scientists contribute data to many publicly-accessible projects, from birdwatchers helping conservation efforts with the e-Bird project, game enthusiasts folding proteins for the FoldIt project, to homeowners exploring the microbial diversity in their houses through the Wild Life of Our Homes project. Additionally, projects like the Science Education Alliance - Phage Hunters Advancing Genomics and Evolutionary Science and Tiny Earth engage students in large research projects as part of course-based undergraduate research experiences. Citizen scientists, Riley et al. argue, can also help discover bacteria with novel, useful traits.

Delftia is a genus of Betaproteobacteria first discovered in the city Delft, where bacteria themselves were discovered by Leeuwenhoek. Delftia has genes capable of precipitating gold by excreting a metabolite called delftibactin. Gold in solution as gold chloride is toxic to bacteria, so Delftia has evolved this novel mechanism for precipitating aqueous gold out of solution to nontoxic solid gold nanoparticles. This mechanism has obvious potential uses in gold recycling in used electronics, gold mining, and urban waste, but to date, the existing genetic diversity of Delftia in strain collections is modest. There are only six known species of Delftia. Full genome assemblies exist for four of these species within the National Center for Biotechnology Information database. Discovery of novel Delftia species and their relatives has the potential to better elucidate variations in Delftia genetic sequences, especially within the gold precipitation gene cluster and other industrially and human health related sequences. The more information about these gold precipitation genes, for example, the greater potential for using Delftia or its genetic potential to recycle our electronics and make mining more sustainable.

A colony of Delftia acidovorans. Khalifa et al. (2019).

The Wolfpack Citizen Science Challenge for Spring 2018 was a collaborative project to document the presence and genetic diversity of Delftia spp. across the North Carolina State University campus and create a scalable and interdisciplinary model to continue learning about this and other organisms. In addition to involving students in two introductory courses in the initial data collection, we also involved students in two upper-level courses in the downstream study of the microbes detected during
the Challenge.

Participants were primarily recruited from two courses, ES 100: Introduction to Environmental Sciences (176 students) and LSC 170: First Year Seminar in the Life Sciences: Meet Your Microbes (20 students). However, anyone interested was able to obtain a sampling kit and participate. A post-event survey indicated that 96% of the participants were required to participate as part of a course and that 48% were currently enrolled as Science, Technology, Engineering and Mathematics majors.

Three events were held to create excitement and share results from the challenge. In January, the Challenge was launched with a public event attended by 19 people, in which Goller and Riley shared information about Delftia acidovorans found in sinks, drains and soil and encouraged members of the campus to think critically about the microbial communities around us. In March, the sequencing data were shared with the campus community at an event at which participants used the National Center for Biotechnology Information Basic Local Alignment Search Tool to find regions of similarity between the discovered sequences and those deposited in the National Center for Biotechnology Information database. This Basic Local Alignment Search Tool workshop was attended by 55 people. In April, results of the project were shared at a closing event open to the campus and general public, attended by 30 people. 

Participants registered as teams of up to five members and were provided kits with instructions and materials to collect samples: three swabs and two 50 millilitre conical tubes for soil samples along with gloves, plastic spoons for scooping soil, alcohol swabs to sanitise the soil collection spoons and labels for samples. Approximately 40 kits were distributed and over 150 swab and soil samples were received between 30 January and 14 February 2018. Samples were delivered in person to either the Biotechnology Program teaching laboratories or the North Carolina State University Libraries front desk. Samples were stored in −20°C freezer until ready for metagenomic DNA extraction. Along with physical samples, metadata including location descriptors and latitude–longitude data were submitted online through a customized SciStarter citizen science website. Students’identifying information was removed from samples and a numerical identity was assigned.

Participants were provided with detailed instructions on how to sample environments around the campus and use the sampling kit. Participants were instructed to use the swab to sample a safe location and immediately place the swab in the transport container. Students collected soil samples with the provided tube and spoon while wearing disposable gloves. For processing of samples, students in molecular biology courses were trained in lab safety procedures and given a document detailing the potential hazards and safety procedures used in the teaching laboratory. For all extractions and qPCR reactions, students wore provided disposable lab coats, safety glasses and gloves, and disinfected all surfaces before and after use.

Metagenomic DNA was extracted from samples using the Invitrogen PureLink Microbiome DNA Purification Kit according to the corresponding protocol for swab and soil samples.Soil was transferred from collection tubes to bead tubes with alcohol-sterilised metal scoops. Swab tips were cut off into bead tubes with alcohol-sterilised metal scissors. Samples were lysed and homogenized by heat, bead beating and lysis buffer. After purification, samples were eluted in 50 μl of elution buffer. DNA concentration was determined spectrophotometrically using a ThermoFisher NanoDrop 2000c instrument and normalized to five ng/μl. Samples were matched with descriptive location data in an online spreadsheet using information submitted on the SciStarter website. Isolations were performed by Noah Riley in batches of 12–24 samples.

An Eppendorf epMotion 5075 TC liquid handler was used to set up quantitative real-time polymerase chain reaction DNA amplification reactions with New England BioLabs Luna Universal Probe qPCR reagents, primers and double-quenched probes. Quantitative  polymerase chain reactions were run on a Bio-Rad CFX Connect instrument and data were exported as spreadsheets with cycle threshold values for each reaction. Samples were screened for the quantity of Delftia present using double-quenched, Delftia-specific primers and probe for a portion of the unique gold biomineralisation metabolite production system (the 'gold gene'). Presence and abundance of Delftia were then confirmed with a second set of primers and probe for a putative Delftia-specific toxin–antitoxin sequence unique to Delftia spp.. Reactions were set up in duplicate along with an 8-point, ten-fold dilution standard curve with 'gold gene' standard beginning at 40 pg/μl and toxin–antitoxin sequence standard at 30 pg/μl.

Undergraduate juniors and seniors and first- and second-year graduate students enrolled in an upper-level High-throughput Discovery 8-week lab module programed an epMotion 5075 TC liquid handler with the quantitative polymerase chain reaction script, prepared metagenomic samples for quantitative  polymerase chain reaction and calculated Delftia copy numbers using the quantitative  polymerase chain reaction cycle threshold data. Students were provided a spreadsheet template with detailed explanations and information on the use of a standard curve for calculation of absolute copy numbers of target sequences. Data were shared with students and groups of three to four were tasked with determining copy numbers for one 96-well polymerase chain reaction plate containing: 23 genomic DNA samples tested in duplicate along with an 8-point standard curve and negative buffer only controls. Multiple groups analysed the same samples to confirm the results and copy number trends were further supported by analysing quantitative  polymerase chain reaction data for the same samples with a primer set for the single-copy Delftia-specific toxin–antitoxin sequence. Data were then analysed as a class and shared with Danica Lewis for visualisation and dissemination of the results to participants and the public. Samples with the highest Delftia copy number using both primer sets were selected for further analysis of the unique gold gene sequence.

For 20 samples with high Delftia counts, a portion of the gold gene sequence was amplified using primers Seq7 and Seq8 and the New England Biolabs Q5(R) High-Fidelity 2X Master Mix. The amplified portion of the gold gene was selected because it is highly specific to Delftia and based on current sequence database information, varies slightly between known species and strains, allowing for identification from metagenomic samples. The target Delftia sequence is 1045 base pairs in length. Of the 20 tested samples, 17 produced sufficient PCR product for sequencing and were sent to the North Carolina State University Genomic Sciences Laboratory for Sanger DNA sequencing using primers Seq7 and Seq8. Amplicons (pieces of DNA or RNA that are the source and/or product of amplification or replication events) were sequenced from both directions and sequences were trimmed based on stringent quality settings to match existing sequences in the National Center for Biotechnology Information database. The sequencing data were shared with the campus community at an event at which participants used the National Center for Biotechnology Information Basic Local Alignment Search Tool to find regions of local similarity between the discovered sequences and those deposited in the National Center for Biotechnology Information database. This allowed participants to identify which Delftia species and strains best matched the samples that were sequenced.

The Google Maps Fusion Tables extension was used to create a heatmap of Delftia presence and abundance across campus and Tableau Public software was used to create an interactive map. Participants were invited to explore the data and evaluate which samples had the highest amount of Delftia. Students in the courses involved in sampling and analysis were shown the results and asked to discuss future research questions.

Map showing the sites at which Delftia spp. was sampled on the North Carolina State University Campus. Danica Lewis/Tableau Public.

Over 150 samples were received from participants. Of these, 135 were labeled correctly and matched with the online SciStarter database containing sampling location descriptions and latitude–longitude coordinates. Through quantitative  polymerase chain reaction analysis using primers and probe Seq1, Seq2, and Seq3, 125 samples (92.6%) had detectable quantities of the target Delftia 'gold gene' DNA sequence. Quantities of Delftia within samples were confirmed using the toxin–antitoxin sequence quantitative  polymerase chain reaction primers and probe Seq4, Seq5 and Seq6. The 20 samples with highest Delftia counts were primarily swabs from sinks and drains. In contrast, the samples with the least Delftia DNA tended to be those from soil samples and outdoor locations. However, it is worth reiterating that nearly all of the samples contained some Delftia, a relatively understudied genus of Bacteria.

Riley et al. next compared the Delftia gold gene sequences in the samples to those of sequenced strains. Collectively, the sequences from their samples were most similar to those of Delftia tsuruhatensis strain CM13, Delftia acidovorans strains ANG1 and SPH-1, or Delftia acidovorans strain RAY209. Differentiation between Delftia acidovorans strains ANG1 and SPH-1 was not possible as each matched query had the same identity, query coverage and E value results for both strains. However, for strains of Delftia tsuruhatensis CM13 and Delftia acidovorans RAY209, the sequences matched with highest probability to each, respectively. None of the samples were close matches for the other sequenced Delftia species of Delftia deserti, D. lacustris, Delftia litopenaei, Delftia rhizosphaerae, or other strains of Delftia acidovorans and Delftia tsuruhatensis. A total of 14 out of the 17 sequences had less than 97% sequence identity with the Delftia strains they most closely matched.

Riley et al. sought to simultaneously test whether they could engage students campus-wide in a citizen science style microbial research project and in doing so, understand the distribution and diversity of strains of one particular Bacterial genus, Delftia. They were indeed able to engage students from diverse majors across campus. In doing so, they discovered that some sampling sites had many more Delftia counts than did others, that Delftia was relatively ubiquitous and that some of the strains we identified had gold genes that appeared relatively divergent from those known from the literature. Although they were unable to accurately determine the diversity of Delftia strains present, this unanswered question presents a new challenge and opportunity for our citizen science and Delftia research efforts.

Collectively, the quantitative  polymerase chain reaction, Sanger DNA sequencing and Basic Local Alignment Search Tool comparison results showed that strains of Delftia are diverse, abundant and frequent (found at many sites) in environments in and around the college campus. Based on available genomic sequences deposited in the National Center for Biotechnology Information database and partial sequencing of the highly conserved gold gene, the strains students discovered best matched the reference strains Delftia tsuruhatensis CM13 and Delftia acidovorans ANG1 and SPH-1. However, 14 of 17 samples contained strains that were a 97% or lower match to strains in the National Center for Biotechnology Information database. Riley et al.'s suspicion is that these strains represent uncharacterised genetic diversity among strains in Delftia’s gold gene. However, because Riley et al. sequenced from complex environmental samples they can’t preclude the possibility that some of this variation is due to cases in which the forward and reverse sequences obtained were from different Delftia species or strains in the sample.

The sequenced Delftia gold gene from many of the participant samples matched well to known Delftia species, but some samples matched two different existing strains equally well. For example, samples from 7-1 to 24-1 were equally similar to the strains Delftia acidovorans ANG1 and SPH-1. Clearly further work can be done to sequence additional portions or the entire genomes of these samples to identify what known strain is present or discover a new lineage of Delftia. More extensive community analyses of the samples using both targeted (16S rRNA gene) and whole genome shotgun sequencing would aid in the identification of which microbes associate with the presence of Delftia and the identity of the gold sequences in the environment, respectively. Additionally, high-throughput sequencing approaches such as Hi-C from Phase Genomics or Nanopore single-molecule long-read sequencing can be employed to attempt to sequence and assemble the entire Delftia genome in metagenomic samples positive for Delftia by quantitative  polymerase chain reaction. Ultimately, selective media capable of isolating and identifying Delftia would allow us to increase our collection of Delftia strains for basic functional studies and genome sequencing.

Riley et al.'s sequencing results best matched the species Delftia acidovorans and Delftia tsuruhatensis, both of which have been found in environments similar to those they studied. Delftia acidovorans was originally discovered in soil and has been found in drains, waterspouts and showerheads in the built environment. Delftia tsuruhatensis was first discovered in a wastewater treatment plant and has been found in similar locations along with Delftia acidovorans. The Delftia species Riley et al. did not encounter in their study are species that have so far been associated with more restricted habitats. Delftia deserti has been found to inhabit desert environments, Delftia lacustris in lake water, Delftia litopenaei in pond water, and Delftia rhizosphaerae in the rhizosphere of the Gum Rockrose, Cistus ladanifer, a Plant native to the Mediterranean region. The apparent ubiquity of the genus Delftia hides the reality that individual species appear to show considerable habitat restriction. In the future, it would be interesting to understand which traits and genes of individual Delftia species confer the ability to survive in particular habitats.

It is unclear the extent to which the life history of Delftia in the above habitats is the same as that of Delftia in the built environment of a college campus. Nor is it well understood whether the presence of Delftia in water systems is problematic or potentially beneficial. Like many Bacterial taxa, Delftia species are recorded as opportunistic pathogens that can infect hospitalised or immunocompromised patients. However, there is no indication that Human bodies are a common habitat for this genus. Instead, in buildings such as those we sampled it appears to be much more common in water systems; in drains, showerheads and downspouts. In as much as the ecological conditions of water systems differ greatly, it is possible that a comparative study of water systems, such as those that are or are not chlorinated, might reveal more about the built environment natural history of this organism.

Riley et al.'s approach kindled campus-wide student interest in microbial diversity and molecular biology techniques through the excitement of discovering this unique microbe in places that students frequent on campus. Groups of students from various academic disciplines and courses produced and analyzed samples that contributed to a large public dataset. The findings helped teach the student community about Delftia and also reinforced the importance of the collaborative nature of scientific discovery. The success of this project, in terms of the documentation of Delftia’s distribution helps to validate Riley et al.'s general approach. In addition, this approach has the potential to encourage future students to participate. Riley et al. aim to continue the challenge of accurately identifying new Delftia lineages and engage others by expanding the sampling opportunity to a multi-section first-year English class that is required for all undergraduate students on the campus. Using a similar approach and incorporating the expertise of faculty in the English department, they will engage students in writing tasks related to the project. Additionally, an upper-level metagenomics course will tie into this endeavor by processing, sequencing and analysing the microbial communities in samples with high numbers of Delftia sequences. With relatively minor changes to the course schedules and curricula, 100 more students per semester can participate, learn and contribute to the project. Riley et al. are creating resources that are accessible for other faculty and campuses to implement this project and share findings. For this, students participating in the project are writing The Delftia Book, and Riley et al. have created a group for instructor resources on the QUBES web portal. Liquid handlers can be cost-prohibitive, but less expensive models such as the Opentrons OT-2 are available, and Riley et al. are developing scripts for this instrument. Student groups in lab-based courses can always set up quantitative polymerase chain reactions manually to participate in this project.

As the future plans for integrating this project into courses indicate, enthusiasm for the project was high among Riley et al.'s colleagues and grew as the project proceeded. However, if they are to continue the project it is key that it continues to yield new scientific insights. Fortunately, this seems very likely to be the case. For example, although Delftia abundance was very patchy on campus, Riley et al. have yet to explain what factors account for such patchiness. Additional samples will help to have sufficient coverage across sample types to allow spatial models of Delftia diversity and abundance. In addition, Riley et al.'s results suggest that new variants of the Delftia gold gene and even new Delftia strains remain to be discovered. Conversely, there is a lack of genomic diversity represented in the National Center for Biotechnology Information database. By leveraging the enthusiasm of university students and staff, interconnecting courses and researchers, and using Riley et al.'s model pipeline, new lineages of Delftia can be rapidly identified and studied (e.g., groups of students cloning novel gold gene cluster into a host such as Escherichia coli or Yeast for functional characterisation). This will yield a better understanding of the ecological and environmental significance of these organisms and simultaneously help to connect students and faculty across campus in a common scientific project. Finally, it is of note that Delftia species, while little known, are of potentially great applied importance. In addition, they contain genes that allow many strains to precipitate gold. Given the many waste streams in which gold is present but hard to concentrate, this ability has the potential to be very useful moving forward.

See also...

https://sciencythoughts.blogspot.com/2020/03/latimeria-chalumnae-live-coelocanth.htmlhttps://sciencythoughts.blogspot.com/2020/02/craspedotropis-gretathunbergae-new.html
https://sciencythoughts.blogspot.com/2017/03/five-confirmed-deaths-as-nigerian.htmlhttps://sciencythoughts.blogspot.com/2016/12/understanding-worlds-highest-vascular.html
https://sciencythoughts.blogspot.com/2016/09/faint-companions-discovered-to-two.htmlhttps://sciencythoughts.blogspot.com/2016/03/microhyla-laterite-new-species-of.html
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