Bioleaching cobalt from sulfide ores| COG3 Consortium

Recently, members of the Acidophile Research Team at Bangor University carried out some bioleaching experiments which aimed to leach cobalt from the Captain sulfide ore (from New Brunswick, Canada). Sarah Smith, a geomicrobiologist at Bangor University and one of the collaborators in the COG3 project reports.

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a) Mixed bacterial cultures used to inoculate the bioreactor experiments. b) A bioreactor before the addition of the culture and the ore. c) Adding the culture to the bioreactor experiment. d) The bioreactor at the end of the bioleaching experiment carried out at 45°C.”

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Introducing Alex Mills | Identification Trainers for the Future

At the end of February we waved goodbye to our second cohort of trainees on the Identification Trainers for the Future project. Kristina, Jaswinder, Sophie, Joe and Niki are now off finishing their final projects and starting their careers and we will update you on their progress shortly.

In the meantime, our next few posts will introduce our third and final cohort on the project. Alex, April, Matt and Steph joined us on 6 March, and Laura will be joining us in the next week. Over the next few posts our new trainees will introduce themselves to you. First up is Alex Mills:

Alex Mills - Intro Blog - Photo

Alex Mills

Curiosity and care. This is why I’m doing what I’m doing. I’m fascinated by the natural world and by how best we can conserve it. We rely upon the organisms and systems which constitute our environment for everything: wildlife is our life.

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Focus on fungi in the Wildlife Garden | UK Wildlife

A few weeks ago as the hours of daylight were gradually lengthening, we were cheered by signs of spring growth through the decomposing leaf litter. The leaf tips of Lords and Ladies (Arum maculatum), have been pushing up since the end of December, as well as the smaller spikes of bluebell leaves. First flowers are late this year, compared to the past few years. Snowdrops (Galanthus nivalis) flowered on 2 February, 11 days later than last year, and daffodils (Narcissus pseudonarcissus) appeared on 20 February – 17 days later than last year.

Photograph showing the fungus in the horizontal centre of the image,

Candle-snuff fungus in the woodland area and hedgerow. Photo © Frances Dismore

With few flowers in sight we have carried out surveys of common fungi and the distribution of these common species throughout the garden. Fungi forays are generally associated with autumn – the most productive months for larger fungi such as mushrooms and toadstools. However there are many attractive species present through all seasons and a search early in the new year can be rewarding.

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Endorsing the Science International Open Data Accord | Digital Collections Programme

A growing number of museums are joining open data initiatives to publish their collection databases and digital reproductions online. The Museum has operated a policy of open by-default on our digital scientific collections.

Photograph of Vince Smith, Head of Informatics reading the Science International Data Accord

Vince Smith, Head of Informatics reading the Science International Data Accord

By signing the International Open Data Accord, the Museum recognises the opportunities and challenges of the data revolution and adopts a set of internationally recognised principles as our response to these.

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Using the “Natural History Large Hadron Collider” to tell us about plant diversity

by Sandy Knapp, NHM Department of Life Sciences

The world’s herbaria hold millions of samples of plants, and until recently they have been largely the domain of taxonomists – those scientists who describe diversity. Herbarium taxonomists compare specimens collected in different parts of the world, assess variation and then come to conclusions about what to name as new, and what to call the same. Our ability to talk about plant diversity depends upon this activity – without names, we would be unable to tell each other about distribution – and as so alarmingly today, decline – of the some half a million plant species with which we share the planet.

Herbaria though are often depicted as dry, dusty out-of-date places, not really connected to the dynamic world of today’s societal needs. But actually, a herbarium can be considered a physical database – each plant specimen is a data point – something that occurred somewhere, sometime, with a particular combination of traits. In a study recently published in BMC Biology, Marc Sosef and colleagues show how powerful a resource these herbarium collections can really be, even in the underexplored tropical rainforests.

The data

Using the RAINBIO dataset  – a collaborative, curated (more about that later) database of herbarium specimens from many institutions all collected in tropical Africa – they perform a number of analyses exploring African plant diversity. Heterogenous datasets like these assembled from herbarium specimens – whose collection is by its very nature ad hoc – are sometimes considered to be less than useful for generating solid estimates of things like species richness, rarity, or turnover (but see commentary in BMC Biology). But for many environments, these are all the data we have.

Specimens in the RAINBIO dataset date from 1782 to the present – almost 250 years of data collection. Figure 5 in the paper graphically shows how exploration of Africa unfolded, along the rivers, tragically along the west coast in association with the iniquitous trade in enslaved people, and patchily through colonial activity in the early part of the 20th century. The history of European engagement with Africa unfolding along with the plants sent to collections, first in European and later also African institutions, is a reminder that science is part of society and does not develop outside of it.

Fig5-1024x683Time lapse of botanical collecting history across tropical Africa. Figure 5.

The robustness of the conclusions drawn by Sosef and colleagues is highly dependent upon the curational state of the data themselves. Taxonomic verification of the identities of samples held in RAINBIO dataset is key to this – this requires taxonomists. One of the things that most impressed me about this study was the degree to which data were validated by taxonomic experts – those scientists whose knowledge of whether or not two names in a list represent the same thing or different species, or whether a species described as a tree on a specimen label really is a tree. There have been criticisms of data served through the GBIF network, for example, but such data are only as good as the curation effort expended; to make use of these rich data sources, first catch some taxonomists and have them on the team!

The findings

The functional data analyzed from the RAINBIO dataset is novel and reveals really interesting patterns. The authors show that the proportion of herbaceous to woody plants is at the upper suggested limit (just under half, 44%). This says to me that tropical botanists need to focus on this vegetation layer as well as on those sexy big trees. An interesting comparison would be of rarity of herbaceous versus woody components of tropical vegetation. If Begonia species are anything to go by, herbs can be extremely rare and range restricted indeed!

Shockingly, the average number of collections per 0.5° square in Africa is 1.84 – that is fewer than two plant records in a square 55 kilometers on each side. Some places, of course, are better collected than others, but let’s get out there! The authors use the patterns revealed by their analysis to suggest collecting priorities for tropical Africa – they identify Tanzania, Atlantic Central Africa and West Africa as priority areas for further collecting to increase our knowledge of plant diversity.

But I might argue that looking at Figure 5, we should seriously think about increasing collecting effort at the northern edge of the African tropics – after all, that is the leading edge of climate change and the area where effects will be felt soon as the environment degrades. These aren’t the big rainforests, but these habitats and areas can be canaries for climate change.

Herbaria (and other natural history collections) represent big science – they are the CERN of natural history. These resources represent an unparalleled infrastructure for looking at how plant diversity is distributed, and are our best hope for documenting how it is changing at a global scale. Imagine if governments or private foundations invested in the digitization of all these invaluable resources, pretty straightforward for flat 2D objects like herbarium sheets, more difficult for 3D objects like insects or worms. The infrastructure thus created, especially if investment is also made in its careful curation and verification, would be the most powerful picture, however flawed it might be, of the Earth’s diversity before it is lost forever. We are crazy not to pull together to create this infrastructure to help us predict our plant’s fate.

This blog post was originally published in the On Biology blog

 

 

Your best rockpooling photos | Big Seaweed Search

Seaweed scientist Professor Juliet Brodie tells us about the fantastic photos submitted through the Big Seaweed Search so far.

I’m fascinated by seaweeds and my research includes finding out about their diversity, and the impact of climate change and ocean acidification on their distribution. As part of this, I worked with my colleagues across the Museum to set up the Big Seaweed Search and I’m so pleased to see that lots of you have taken part and have sent your photos in for my research. I’ve just been exploring the first few months of data entered and I’m very excited by what I have seen so far.

Photo showing the seaweeds in the centre, with arrows added to show their location (coral weeds to the right of centre, and calcified crusts to the left of centre)

Some people think seaweeds are dull and brown but I was very taken with this beautiful image of the pink coral weeds (white arrow) and calcified crusts (black arrow) growing together. Photo © Jessica Jennings

In particular, the photographs people have uploaded are excellent as they enable me to tell very quickly whether a seaweed has been identified correctly or not – this is essential for me to be able to use the observations in my research.

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The story behind putting Geography into our collections | Digital Collections Programme

Guest blog by Liz Duffel, Georeferencing Digitiser

Most specimens within the Museum collection have locality information, showing where the specimen was found, on the accompanying label(s). When we are digitising our specimens, we can use that locality information for georeferencing – the process used to give the locality of a specimen geographical coordinates, so that it can be plotted on a map.

Data map with hotspots

A data portal visualisation showing the global distribution of the Museum’s zoological specimens with digital records

This is important because it allows for mapping and modelling, which underpins research on anything from species distributions and relationships, to environmental changes or targeting conservation practices.

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