Category: Biology

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Wood Wide Web by Gauri Sirur

Fungal filaments
Humming under forest floor
Trees communicate.

By Gauri Sirur

Trees communicate with each other through an underground network of mycorrhizal fungi. The fungal strands colonize the tree roots, and form a web connecting the roots to each other.

The relationship between the fungi and trees is usually symbiotic. The fungi take a share of the sugars that the trees produce during photosynthesis. In return, the trees receive nutrients such as phosphorous and nitrogen that the fungi synthesize from the soil.

Through the network, trees share food — carbon-rich sugars, nitrogen, and phosphorous — with other trees. They also send out warning messages about predators such as aphids and caterpillars. Or about pathogen attacks. This buys their neighbors time to activate their defenses.

All is not sugar and spice, however. Both trees and fungi try to extract the maximum amount of nutrition from the other while giving the minimum in return.

Trees are more likely to help their kin than an unrelated tree. Or to release toxic substances to harm an unwanted neighbor.

Dr. Suzanne Simard, a scientist at the University of British Columbia, discovered the fungal network in 1997. She dubbed it the “Wood Wide Web.”

Further reading:

‘Wood Wide Web mapped for the first time’ – Science article.

‘Uncovering the hidden language of trees’ – Suzanne Simard interview.

‘Net transfer of carbon between ectomycorrhizal tree species in the field’ – Suzanne Simard’s 1997 research paper first documenting the fungal network.

Gauri Sirur enjoys writing about nature, family, and anything that intrigues her. You can find her writing at gaurisirur.wordpress.com and gaurisirur.medium.com.

This sciku was originally published by Gauri Sirur on Medium.com here.

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Mistletoe

festive parasites
regulating virulence
to preserve their hosts

Mistletoe is a parasitic plant often found growing on hardwoods, such as apple trees. Whilst able to photosynthesize itself, the majority of a mistletoe plant’s water and nutrients are taken from its host, putting strain on the host plant.

The burden of parasitism can be particularly hard on the host when environmental conditions are tough, for instance during a drought. Research by Nabity et al. (2021), however, has shown that the desert mistletoe (Phoradendron californicum) is able to adjust the balance between autotrophy (the amount it obtains resources for itself through photosynthesis) and heterotrophy (the amount it takes resources from its host).

During dry periods the researchers found that desert mistletoe plants increased the amount of photosynthesis they performed, limiting the burden they place on their environmentally stressed host, the velvet mesquite (Prosopsis velutina). In this way mistletoe plants increase the chances of their host plants surviving the harsh environmental conditions and, as a result, increase their own chances of survival.

The researchers also demonstrated evidence of competition for xylem resources between mistletoe plants on the same host, some of the first evidence of intraspecific competition in parasites. The mistletoe plants are able to detect other mistletoe plants on the same host and can adjust their virulence accordingly. Possible ways that mistletoe could detect one another include via scent (chemical compounds released through a plant’s pores) or through chemical compounds traveling along the host’s xylem.

The research also suggests that levels of relatedness between mistletoe plants sharing the same host may even affect virulence. More research is needed to clarify this, however, and to investigate whether the plants can actually detect relatedness or whether mistletoe’s method of seed dispersal simply means that plants sharing the same host are likely to have higher levels of relatedness than mistletoe plants on separate hosts.

Further reading: http://dx.doi.org/10.1016/j.cub.2021.01.034

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Public Health by Dr Alex Stockdale

In mid-2021 The Sciku Project teamed up with the Literature and Science Hub at the University of Liverpool to run the ‘Research in Verse Poetry Competition’, open to staff and postgraduate research students across the university to submit poems about their research subject. The competition saw poems addressing all sorts of topics, ranging from gravity to slavery to life in the lab.

Dr Alex Stockdale’s poem ‘Public Health’ was praised by the judges as a notable entry:

Public Health

In a long corridor wailing
Bite
The virus knuckles and grasps
Enters cells
At birth was I living with him
His genome nestling in mine

Now fluid fills the belly
Tumour fills my liver
Hope left this station
Staring out the window
At a blue calm sky on a roaring hot day in Malawi

Too late they said
Too hard
Nothing more to say
I don’t have much time left to live but I want you to know
It could have been prevented

Background

This poem is about my research into liver disease in Blantyre, Malawi. We found that over 70% of liver cancer is caused by hepatitis B. Infection can be prevented by vaccination starting at birth and by antiviral treatment for pregnant women. Currently, vaccination starts at 6 weeks of age and my research is exploring whether this is sufficient to prevent transmission. This poem draws attention to the many people who present with late stage liver cancer in Malawi, for whom median prognosis is only 6 weeks at diagnosis, and for whom hepatitis B infection remains a preventable disease. 

Dr Alexander Stockdale is a clinical researcher at the University of Liverpool with a focus on viral hepatitis and HIV in sub-Saharan Africa.

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Mammoth document by Dr Janette Greenhalgh

In mid-2021 The Sciku Project teamed up with the Literature and Science Hub at the University of Liverpool to run the ‘Research in Verse Poetry Competition’, open to staff and postgraduate research students across the university to submit poems about their research subject. The competition saw poems addressing all sorts of topics, ranging from gravity to slavery to life in the lab.

Dr Janette Greenhalgh’s fascinating poem using a repeating haiku structure was a notable entry:

Mammoth document

Mammoth document
Brim-full of words, so URGENT!
Fight, flight, cup of tea?

URGENT document
Mammoth in the room, storming
Kettle shrieks volumes

Words, words, words and more
Unwrap, repurpose, rebind
With fight, flight and tea

Mammoth document
Brim-full of our words. Job done!
Outside, sweet birdsong

Background

Our research is mainly commissioned by the NIHR Health Technology Assessment programme on behalf of the National Institute for Health and Care Excellence (NICE). Our core work is to provide a critique of evidence submissions to NICE from pharmaceutical companies for the clinical and cost effectiveness of new drugs. We have multi-disciplinary teams working on each report (clinical effectiveness reviewer, statistician, economic modeller, clinical expert). The timelines are very short – we have 8 weeks from receipt of the evidence to submitting our critique to NICE.

Dr Janette Greenhalgh is a Senior Research Fellow with the Liverpool Reviews and Implementation Group, Department of Health Data Science, Institute of Psychology and Health. You can connect with her on Twitter here: @drjanetteg

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Yearning by Dr Kate Baker

In mid-2021 The Sciku Project teamed up with the Literature and Science Hub at the University of Liverpool to run the ‘Research in Verse Poetry Competition’, open to staff and postgraduate research students across the university to submit poems about their research subject. The competition saw poems addressing all sorts of topics, ranging from gravity to slavery to life in the lab.

Dr Kate Baker’s nostalgic haiku on the perils of academic career progression was a notable entry:

Yearning

Test tubes and pipettes?
A life spent on email
yearning for the bench

Background

It’s not so much my research as the transition from postdoc to principal investigator that inspired my poem.

Dr Kate Baker is a Senior Lecturer and leader of The Bakery – an applied microbial genomics laboratory at the University of Liverpool. You can connect with her on Twitter here: @ksbakes.

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Vaccines and Protection by B.R. Shenoy

Vaccines protect us
Trigger an immune response
Prevent infection

by B.R. Shenoy

Mechanism of Action of Vaccines

“A vaccine works by training the immune system to recognize and combat pathogens, either viruses or bacteria. To do this, certain molecules from the pathogen must be introduced into the body to trigger an immune response.

“These molecules are called antigens, and they are present on all viruses and bacteria. By injecting these antigens into the body, the immune system can safely learn to recognize them as hostile invaders, produce antibodies, and remember them for the future. If the bacteria or virus reappears, the immune system will recognize the antigens immediately and attack aggressively well before the pathogen can spread and cause sickness”

— PublicHealth, ‘How Vaccines Work’

B.R. Shenoy is a biochemistry and chemical toxicology, M.S. She is a contributing writer for The Good Men Project. Her work has also appeared in Scary Mommy, Positively Positive, and Idle Inks. She is a content creator on Medium. You can catch up with her on Twitter @Shenoy100.

This sciku was originally published on Medium: https://medium.com/illumination/vaccines-and-protection-a-sciku-ca1491e36b13

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Darwin’s Finches

islands diverging
beaks for seeds and bugs and blood
letters rearranged

Darwin’s finches are a group of 18 species of passerine birds found across the Galápagos Islands (hence their other name of Galápagos finches). The group are a poster child for Darwin’s theory of evolution by means of natural selection. During his voyage on the HMS Beagle he collected specimens from what later turned out to be 12 of the 18 species, although Darwin himself didn’t realise the significance at the time, not realising they were all types of finch (ornithologist John Gould corrected him about the species) and not recording which islands they came from (he was later able to correctly assign them based on the notes of others on the voyage).

As the finches colonised the islands and began to adapt to the varied habitats and food resources available, the different groups diverged from each other, resulting in the separate species we see today. The finches themselves have a huge variety of forms (likely leading to Darwin’s confusion), most notably in their beak shapes and sizes. Their beaks are highly specialised to the food sources available on the different islands, with different species feeding on nuts, seeds, flowers, nectar, leaves, cacti, and invertebrates (including insects, parasites, larvae and spiders).

Perhaps the strangest of all is the Vampire Ground Finch (Geospiza septentrionalis) which feeds on the blood of other birds such as blue-footed boobies and Nazca boobies. It’s theorised that this behaviour evolved from mutualistic behaviours where the finch would clean parasites from the plumage of larger birds. These days their sharp beaks are used to peck their victim’s skin until it starts bleeding and the finches feed on the blood. Their unpleasant behaviours don’t stop there, however, as they steal eggs and roll them into rocks to break the shells, and they’ll also eat guano – excrement from seabirds. Since fresh water is scarce on their home islands (Wolf Island and Darwin Island), they also feed on nectar from Galápagos prickly pear flowers.

Molecular studies of Darwin’s finches suggests that the timing and spatial expression of at least four genes are responsible for the differences in beak structure, alphabetic changes that led to anatomical changes: BMP4 (which encodes Bone morphogenetic protein 4), CaM (which encodes Calmodulin), ALX1 (which encodes ALX homeobox protein 1), and HMGA2 (which regulates the expression of other genes).

A note about the sciku: this sciku has been written using a scale and focussing structure – narrowing in from the vast islands to the beaks to the individual letters of DNA. Have you ever tried writing sciku with a focussing structure? If so, how did you get on? Let us know in the comments below!

Interested instances of evolution in action? Check out this sciku by Prof Matthew J. James on the classic example of evolution, the Peppered Moth: Dark Moths.

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Urban parakeet by Dr Matt Geary

Urban parakeet
Feeds in small parks and gardens
Missing from forests

By Matt Geary

As with many islands around the world, the island of Hispaniola in the Caribbean is home to a number of bird species found only there. Hispaniola is divided between two countries, Haiti and the Dominican Republic. Both countries have experienced severe environmental change since European colonisation, including considerable forest loss and agricultural expansion. Hispaniolan parakeet (Psittacara chloropterus) is hard to find across the Dominican Republic but a considerable population lives in the capital city, Santo Domingo. Our work explores how these vulnerable island endemics use the urban environment.

In 2019, our research team spent three months walking through parts of the city where parakeets are found, counting birds as well as measuring the natural environment around them. They covered 60 1 km2 squares of Santo Domingo, visiting each square three times. As well as looking for parakeets, they recorded sightings of another endemic, Hispaniolan woodpecker, a species which makes cavities in trees where parakeets are potentially able to nest. The team were also on the lookout for parakeet nest sites in trees and buildings.

Hispaniolan parakeet (Psittacara chloropterus). Image credit: Martingloor.

The population in the city is certainly large. We counted around 1500 birds at a communal roost site in the city centre and saw lots of birds on our surveys. We found that parakeet distribution within the city was related to the number of different tree species within the square and saw more parakeet groups where there were more small greenspace patches. This suggests Hispaniolan parakeets are using street level green spaces like small parks and gardens for foraging rather than relying on large areas of vegetation. We only found three locations where parakeets were nesting, all of which were previously know – one palm tree and two communal roosts in buildings.

This species certainly needs some support across the island of Hispaniola and we hope that by improving our knowledge about this population, which may be the largest remaining, we can help to improve the outlook for the species as a whole. Our work continues on this species and other Hispaniolan endemics. @AndreaThomen is putting the miles in with survey work across the island for her PhD research so we hope to have much more to report in the near future.

Further reading: Geary, M., Brailsford, C.J., Hough, L.I., Baker, F., Guerrero, S., Leon, Y.M., Collar, N.J. and Marsden, S.J., 2021. Street-level green spaces support a key urban population of the threatened Hispaniolan parakeet Psittacara chloropterus. Urban Ecosystems, pp.1-8. https://link.springer.com/article/10.1007/s11252-021-01119-1

Dr Matt Geary (https://mattgeary.github.io/) is a Conservation Ecologist working in the Conservation Biology Research Group at the University of Chester. Twitter: @MattGeary

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The Early Impacts of COVID-19 on Australian General Practice by Dr Michael J. Leach

General practice
as COVID strikes—workloads rise
as revenues fall

by Dr Michael J. Leach

The coronavirus disease-19 (COVID-19) pandemic has affected populations and industries in multifarious ways. For more than a year now, global viral spread and associated lockdowns have driven major health and economic crises. While industries such as travel and entertainment have experienced dramatic reductions in both workload and revenue, the situation in the health care industry is more complex.

In a health services research study, Kippen et al. (2020) explored the early impacts of COVID-19 on Australian general practice through a national online survey. This survey was distributed to 4,891 Australian general practice supervisors on 14 April 2020—less than one month after the World Health Organization upgraded the COVID-19 epidemic to a pandemic on 11 March 2020. The cut-off date for survey completion was 13 May 2020. Overall, 572 of the 4,891 general practice supervisors responded, giving a relatively good physician response rate of 12%.

Of the 572 respondents, 61% reported an increased overall workload during the pandemic while 77% reported reduced practice revenue. Increased workloads related to the implementation of new hygiene practices and clinical regimens, heightened community anxiety, and higher volumes of phone calls. Reduced practice revenues, meanwhile, stemmed from additional administrative work, additional clinical work that could not be reimbursed through the government in the usual way, and the need to purchase new resources such as disinfectant and personal protective equipment. Such changes have adversely affected the viability of Australian general practice—a cornerstone of the health care sector, especially during a pandemic.

The original research article described here is available open access online:
Kippen R, O’Sullivan B, Hickson H, Leach M, Wallace G. (2020). A national survey of COVID-19 challenges, responses and effects in Australian general practice. Australian Journal of General Practice. 49(11): 745-751. https://www1.racgp.org.au/ajgp/2020/november/national-survey-of-covid-19-challenges

Michael J. Leach (@m_jleach) is an Australian epidemiologist, biostatistician, and poet based at the Monash University School of Rural Health. His debut poetry collection is Chronicity (Melbourne Poets Union, 2020).

Check out more sciku by Michael, including ‘The Core Correlate of COVID-19 Vaccine Acceptance‘, ‘Drug-Induced Hip Fractures‘, ‘The Psychopharmacological Revolution‘, ‘Quality of Life at Seven Years Post-Stroke‘, ‘The Burden of Bushfire Smoke‘, and ‘Australian Science Poetry‘ with science communicator Rachel Rayner. Michael also has another Covid-19-related sciku published in Pulse which is well worth checking out: ‘flu shot announcement‘.

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Owls of the Eastern Ice by Jonathan Slaght – Book Review

a fish owl
on an icy river bank
grabs more than fish

by Jon Hare.

Jonathan Slaght’s book “Owls of the Eastern Ice” is part natural history and part adventure story. The natural history focuses on Blakiston’s fish owl, the largest living species of owl. The adventure focuses on Dr. Slaght’s research on the Blakiston’s fish owl in the Primorye territory of Russia – a rugged region in the Far East bordering the Sea of Japan, North Korea, and China. The region is home to Amur tigers, Asiatic bears, masu salmon, and Blakiston’s fish owls. The region is also home to villages, logging companies, and loners – all living off of the land.

Dr. Slaght’s task is to understand the owl and then develop a conservation plan that the logging companies and local communities can support. This is a well written narrative that is as much a story of the human condition as it is a description of the work necessary to better understand and conserve the fish owl.

Slaght, J.C. 2020. Owls of the Eastern ice: A quest to find and save the world’s largest owl. New York: Farrar, Straus and Giroux, 368 pp. ISBN: 9781250798718

Dr. Jon Hare is a scientist who works in Woods Hole, Massachusetts. His research background is fisheries oceanography and climate change impacts on marine fisheries. Check out Jon’s previous sciku ‘Varves’, ‘Cobwebs to Foodwebs’, ‘Signs of Spring’ and ‘Glacier Mice‘.

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The Core Correlate of COVID-19 Vaccine Acceptance by Dr Michael J. Leach

vaccine acceptance
correlates with a belief
in the greater good

by Dr Michael J. Leach

During 2020 and 2021, acceptance of coronavirus disease-19 (COVID-19) vaccines has been among the most topical areas of health science research. As COVID-19 vaccine availability continues to rise worldwide in a global effort to combat the ongoing coronavirus pandemic, more and more people are faced with the question of whether or not to get vaccinated. Even when an approved COVID-19 vaccine is readily available to a particular subgroup of the global population, a high level of vaccine uptake cannot be guaranteed. For one reason or another, individuals within the population may be hesitant to roll up their sleeves to receive the COVID-19 vaccine.

In a UK population-based study, Freeman et al. (2021) investigated factors related to vaccine hesitancy through an online survey completed by 5,114 adults over September-October 2020. The research team measured vaccine hesitancy within the study population using a specially developed tool—the Oxford COVID-19 vaccine hesitancy scale. While 71.7% of surveyed adults expressed willingness to accept the COVID-19 vaccine, 16.6% were very unsure about vaccination and 11.7% showed strong vaccine hesitancy.

Among the various beliefs, views, attitudes, and past experiences considered by the researchers in their analysis, the factor most strongly correlated with vaccine hesitancy was whether or not individuals believed in the collective importance of COVID-19 vaccination. An individual’s belief in the collective importance of COVID-19 vaccination is defined as the recognition that getting vaccinated protects the community and saves lives. This belief is consistent with the critically important field of public health and with the idea of doing something—in this case, getting vaccinated—for ‘the greater good’.

Based on the results of their study, Freeman et al. suggest that public health messages highlighting the societal benefits of vaccination could be broadcast in an effort to increase belief in the collective importance of COVID-19 vaccination and, thus, improve vaccine acceptance and uptake.

The original research article described here is available open access online:
Freeman D et al. (2021). COVID-19 vaccine hesitancy in the UK: the Oxford coronavirus explanations, attitudes, and narratives survey (Oceans) II. Psychological Medicine 1–15. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7804077/pdf/S0033291720005188a.pdf

Michael J. Leach (@m_jleach) is an Australian epidemiologist, biostatistician, and poet based at the Monash University School of Rural Health. His debut poetry collection is Chronicity (Melbourne Poets Union, 2020).

Check out more sciku by Michael, including ‘Drug-Induced Hip Fractures‘, ‘The Psychopharmacological Revolution‘, ‘Quality of Life at Seven Years Post-Stroke‘, ‘The Early Impacts of COVID-19 on Australian General Practice‘, ‘The Burden of Bushfire Smoke‘, and ‘Australian Science Poetry‘ with science communicator Rachel Rayner. Michael also has another Covid-19-related sciku published in Pulse which is well worth checking out: ‘flu shot announcement‘.

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Indirect Inequality

Covid cares not for
the racial disparity
of heart disease

It was well-known before the pandemic that different racial/ethnic populations in the United States had different burdens of cardiovascular disease, with Black populations the worst affected.

The Covid-19 pandemic, however, has found ways of making bad things even worse, with deaths from heart disease and cerebrovascular disease rising across the whole of the USA. Yet new research by Wadhra et al. (2021) suggests that these increases aren’t evenly distributed across all racial/ethnic populations. Black, Asian and Hispanic populations have experienced a much larger relative increase in deaths (~19%) than the non-Hispanic White population (~2%).

A number of factors could be combining to result in this disproportionate impact of the pandemic on different racial/ethnic groups, including “reduced access to healthcare services, increased health system strain, and hospital avoidance due to fear of contracting the virus in high-burden areas. In addition, inequities in the social determinants of health that are associated with cardiovascular risk, such as poverty and stress, have likely worsened for these groups.”

Whilst depressingly unsurprising, these results make it clear that the United States urgently needs public health and policy strategies to “monitor and mitigate the short- and long-term adverse effects of the pandemic on the cardiovascular health of diverse populations.”

Original research: https://doi.org/10.1161/CIRCULATIONAHA.121.054378

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Xenopus Enrichment

Smooth frogs and fake plants
embracing in the water.
Happiness is here.

The African Clawed Frog, Xenopus laevis, is a common laboratory model species of amphibian, used in research primarily for their embryos and eggs. Yet despite their popularity little attention has been given to the housing and husbandry – what is the best way to keep the African Clawed Frog?

Recently, however, things have begun to change as more attention is being given to the welfare of ‘lower’ vertebrates and invertebrates. Indeed, in 2016 we published research demonstrating that a darker tank background resulted in lower levels of corticosterone (a stress hormone), lower instances of stereotypical behaviour and less change in body mass (Holmes et al, 2016). The results suggest that darker backgrounds are better for African Clawed frog welfare in captivity (check out the sciku ‘Clawed frogs indicate‘ for more information about the study and the likely reasons behind the preference).

Now in 2021 new research has been published by Ramos and Ortiz-Díez that examines X. laevis preferences for types of physical enrichment within their tanks. The researchers provided tanks of frogs with artificial plants and opaque PVC tunnels and checked on the frogs three times a day for 6 weeks to see where in the tanks they were spending their time – with the plants, tunnels or in the open areas of the tanks. The results indicate that the frogs preferred the plants 40% more than the tunnels, although both were preferred over the areas of open space in the tank.

As research into the welfare of amphibians gains momentum it’s good to see more work focussing on this common laboratory animal and how it’s kept in captivity. Particularly warming is that in the experimental methods the researchers specifically state that tanks with dark sides and bases were used to reduce visual stress, referencing our earlier work.

Original research: https://doi.org/10.1177%2F00236772211011290

A note about the sciku: The phrase ‘smooth frogs’ that starts the poem is a reference to the meaning of the name laevis – smooth (the word Xenopus means ‘strange foot’).

Interested in African clawed frogs? Check out these other Xenopus sciku: ‘Clawed frogs indicate‘, ‘Have frog, will travel‘, ‘Fungal culprit‘ and ‘Reservoir or predator‘.

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Saba, the morning breeze by Dr Jolene Ramsey

We know you were small
Preying on Proteus too
Surprise, DNA!

by Dr Jolene Ramsey

Bacteriophages, or phages, are the viruses that infect bacteria. They come in different shapes and sizes, but are often icosahedral (spherical) and tailed. A tailed phage is structured like a filled lollipop, where the candy represents the phage head, the filling represents the nucleic acid genome, and the stick is like the tail. The overwhelming majority of phages scientists and students have discovered up to this point are tailed with a DNA genome, largely due to bias in our sampling methods. Recent investigations suggest many phages with RNA genomes remain to be isolated, and they were hypothesized to be small and round, similar to the ones that are already known. We want to find them.

In a very focused hunt, we looked for small RNA phages against the human opportunistic pathogen Proteus using a filtration selection method. After a few rounds of selection, there was a prime candidate that was definitely small, but it didn’t pass the other tests that define RNA phages. It was a puzzle. For clues, we looked at the phage shape in the electron microscope. To our astonishment the phage had a tail and a very small head! We immediately verified that it had a DNA genome as well. Though the search was a failure, we put phage Saba in the arsenal for use in other projects. To fully survey the diverse kinds of phage in the environment we will need to develop and refine targeted and general protocols for phage isolation. This will give us the most accurate picture of the phage universe.

Original research: https://doi.org/10.1128/MRA.01094-19

Jolene Ramsey studies bacterial viruses (phage) as a Center for Phage Technology postdoctoral researcher. She tries to understand how phages orchestrate their escape plan at the molecular level. You can catch up with her on Twitter: @jrrmicro

Enjoyed Jolene’s sciku? Check out her excellent sciku ‘Privateer, the phage’, ‘TF gets in on the bud’, ‘Click click go!’ and ‘The Phriendly Phage‘.

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The Phriendly Phage by Dr Jolene Ramsey

Phage are phriends, not phood
Not Phriendly to host, but nice
Plaques phor lab hunters

By Jolene Ramsey

Vibrio natriegens is an environmental microbe that naturally resides in marine habitats, including brackish waters and salty marshes. If you Google this bacterial species, all the top hits will tout its ‘fast’ growth. Unusual among bacteria, but common with other vibrios, V. natriegens has a  >5 Megabase genome split across two chromosomes. It also has a high count of total ribosomes, the cellular machines that make protein. As a non-pathogenic environmental organism, researchers are exploring its use in various biotechnology applications, including as a protein production system. This is one reason some are hoping V. natriegens will become the next lab workhorse in molecular and industrial microbiology that could even rival E. coli.

With an interest in improving the resources available to use in this field of research, we decided to look for bacteriophages that target V. natriegens. Bacteriophages, or phage, are the viruses that infect bacteria. Because phage rely so heavily on their host cell to copy themselves, they turn out to be extremely useful tools for probing how the cell works. As a kind of natural predator, phages can be found everywhere the host lives. The phage this Sciku is about, named Phriendly, was found in a sample collected by a college student brand-new to research on a trip to the beach.

The phage hunt process involves layering spots of environmental samples on top of growing bacteria, then looking for clear spots where the bacteria did not grow (or died due to infection) called plaques. A few of the beach samples yielded these plaques. One was a hazy, weak plaque that was difficult to propagate. We nicknamed it ‘problem phage’. In contrast, another had large, clear plaques that appeared quickly and consistently. We dubbed it the ‘friendly phage’. Following our cute tradition, we replace all ‘f’ sounds with the ‘ph’ used in the word phage to come up with the name Phriendly. Along with others, Phriendly is in a collection of phages we hope can be tools to better harvest the great potential its host microbe has for advancing biotechnology.

Original research: https://doi.org/10.1128/MRA.01096-19

Jolene Ramsey studies bacterial viruses (phage) as a Center for Phage Technology postdoctoral researcher. She tries to understand how phages orchestrate their escape plan at the molecular level. You can catch up with her on Twitter: @jrrmicro

Enjoyed Jolene’s sciku? Check out her excellent sciku ‘Privateer, the phage’, ‘TF gets in on the bud’, ‘Click click go!’ and ‘Saba, the morning breeze’.

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The Masterplan by Dr Lisa Holmes

Zoo science prevails

Conservation cannot wait

“Prevent extinction”

By Lisa Holmes

Celebrating its 90th year, Chester Zoo is one of the world’s leading zoo’s, housing more than 500 species and dedicated to their mission of “Preventing extinction”.

This week marks the release of their new 10 year Conservation Masterplan; a bold vision with the aim to tackle the global extinction crisis using six key targets:

  • Preserve options for future conservation for an additional 150 species through conservation breeding and propagation.
  • Halt or reverse the decline of 200 highly threatened populations of plants and animal species in the wild.
  • Improve landscapes for wildlife totalling 250,000 hectares.
  • Train 5,000 conservationists to deliver positive change for wildlife.
  • Empower 10 million people to live more sustainably.
  • Influence change in five major policy areas for wildlife.

Chester Zoo has an integrated approach to conservation using the skills and expertise of their staff, conservation partners, students, academics and supporters.

Dr Lisa Holmes is the Lead Conservation Scientist for Behaviour and Welfare at the zoo. She works closely with the animal curators and teams to provide an evidence-base for management decisions. With her team of staff and students, she conducts research to monitor the wellbeing of all species and is developing tailored welfare assessments for use within the zoo. She is also Vice-Chair of the Animal Welfare Working Group for the European Association of Zoos and Aquaria (EAZA).

Check out Lisa’s previous sciku ‘A Zoo Without Bars’.

You can read Chester Zoo’s Conservation Masterplan by clicking on the image below:

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Rigs to Reefs

Oh puffing pig fish –
torn between disturbance and
piscine temptations.

Noise pollution from oil and gas drilling platforms can have huge negative impacts upon marine life. However, such rigs can also act as artificial reefs, providing shelter and a hard substrate for predators and prey alike. Moreover trawling isn’t permitted close to rigs, meaning that the seabeds around them are mostly untouched.

Harbour porpoises, Phocoena phocoena, have previously been shown to change their behaviour or avoid areas as a result of unnatural noise levels. Yet a recent study by Tubbert Clausen et al. (2021) has revealed that the temptations of high prey availability can overcome such affects. The team use 21 acoustic loggers, placed on the seabed for up to 2 years to monitor noise levels and harbour porpoise activity.

They found that despite the high noise levels from the largest rig in the Danish North Sea, the porpoises were still found close to the rig, emitting echolocation noises that indicate they were hunting for fish. The platform’s artificial reef effect appeared to increase fish numbers which drew the porpoises closer.

The findings suggest that as platforms come to the end of their lifespans, they could be partially left in place to continue acting as artificial reefs – the rigs-to-reefs concept.

The first line of the sciku refers to two names for the harbour porpoise:

– The ‘pig fish’ from the Medieval Latin porcopiscus, a compound of porcus (pig) and piscus (fish).

– The ‘puffing pig’ which comes from the noise the porpoises makes when surfacing to breathe.

Original research: https://doi.org/10.1002/2688-8319.12055

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Click click go! by Dr Jolene Ramsey

Galaxy applied
Eyes scan Apollo data
To annotate phage

By Jolene Ramsey

Studying the genetic makeup of an organism helps us understand how they tick. Scientists often make precise notes about the position and function of important features within a genome, called annotation, akin to marking and reviewing the restaurants on a city map. Viruses tend to have smaller genomes, but they are packed with information. We annotate the genomes of bacteriophages, the viruses that infect and kill bacteria, to reveal their genetic secrets. While there are automated annotation programs, manual review by human eyeballs is necessary to ensure high quality outcomes. With the number of interesting new phage genomes rising daily, the need for user-friendly tools to analyze their genomes has grown as well.

Using our curated toolbox in an open-source, online bioinformatic portal called Galaxy (https://cpt.tamu.edu/galaxy-pub), features common to bacterial and phage genomes can be spotted and cataloged by novices and experts. There are many feature types, each one detected by a different tool. Instead of manually passing the genome through each tool, we are able to speed up and standardize the process using automatic pipelines that run a prescribed list of analyses. We can visualize the results in context using another linked platform called Apollo, and also compare to known genomes. The coupled Center for Phage Technology Galaxy and Apollo suite have allowed us to annotate >130 bacteriophage genomes, and train many students and researchers along the way.

Original research: https://doi.org/10.1371/journal.pcbi.1008214

Jolene Ramsey studies bacterial viruses (phage) as a Center for Phage Technology postdoctoral researcher. She tries to understand how phages orchestrate their escape plan at the molecular level. You can catch up with her on Twitter: @jrrmicro

Enjoyed Jolene’s sciku? Check out her excellent sciku ‘Privateer, the phage’, ‘TF gets in on the bud’, ‘The Phriendly Phage’ and ‘Saba, the morning breeze’.

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Mapping Seagrass Loss

Quantifying our
marine meadows – past, present.
A threadbare carpet.

Everyone knows their own science interests, the areas of research that they find thought-provoking. Sometimes I think that there are also subjects that we don’t realise we find fascinating. I never knew I was interested in seagrasses but this is the third sciku I’ve published about them, the second that I’ve written myself. It’s curious that I wouldn’t have known this about myself before today when this research paper caught my eye.

Seagrasses are hugely important ecosystems. In the sciku ‘Forgotten value’ I wrote about how seagrass meadows provide a nursery habitat for over a fifth of the world’s largest 25 fisheries. And as Dr Phil Colarusso showed with his sciku ‘Blue Carbon’, seagrass meadows collect and sequester large amounts of carbon, removing it from the global carbon cycle. As a result seagrass meadows are referred to as blue carbon habitats, along with salt marshes and mangroves.

Today’s sciku is based on a study by Green et al (2021), which examines the historical loss of seagrasses from the waters around the United Kingdom. By scrutinising multiple accounts from as early as 1831 and using data collected from 1900 onwards the researchers were able to estimate the UK’s seagrass losses. It makes for sobering reading:

“At least 44% of United Kingdom’s seagrasses have been lost since 1936, 39% since the 1980’s. However, losses over longer time spans may be as high as 92%.”

The research shows that the UK currently has only 8,493 hectares of seagrass meadows remaining. That’s approximated 0.9 Mt (million tonnes) of carbon, equivalent to around £22 million in the current carbon market. Whilst that may seem a lot, it’s worth considering that historic seagrass meadows could have stored 11.5 Mt of carbon, supporting around 400 million fish.

These losses are catastrophic but the information from this study can be used to inform future monitoring and restoration efforts. What’s more, by quantifying the benefits we gain from seagrass meadows as well as what we’ve lost from their disappearance, the findings also provide an impetus for improved conservation efforts, beyond ‘softer’ arguments such improving biodiversity.

Original research: https://doi.org/10.3389/fpls.2021.629962  

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Privateer, the phage by Dr. Jolene Ramsey

What’s in the EM?
A crayon? A tailocin?
No, that’s Privateer!

By Jolene Ramsey

Proteus mirabilis is an opportunistic human pathogen, causing a large proportion of urinary tract infections. These infections are particularly severe in the elderly, and their treatment is recalcitrant to many antibiotics. There is great interest in using the natural predators of Proteus, their viruses (bacteriophages), to mitigate this issue. However, not many Proteus bacteriophage have been identified or characterized yet.

In our recent study (Corban & Ramsey, 2021), we describe a new phage called Privateer that infects and kills Proteus mirabilis. We first saw this phage in the electron microscope (EM) and noticed its unusual elongated head shape. Privateer has some interesting genes that seem to be common only among the closest related phages. Studies like these are the foundation for future applications combating multi-drug resistant bacterial problems.

Original research: https://doi.org/10.7717/peerj.10645  

Jolene Ramsey studies bacterial viruses (phage) as a Center for Phage Technology postdoctoral researcher. She focuses on their explosive escape from the host cell after a successful infection. You can catch up with her on Twitter: @jrrmicro

Enjoyed Jolene’s sciku? Check out her other sciku ‘Click click go!’, ‘TF gets in on the bud’, ‘The Phriendly Phage’ and ‘Saba, the morning breeze’.

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Sawfish Decline

Shout from the rostrum:
‘Poor Carpenters in the soup!’
Such dentistry snared.

Tracking declining animal populations can be tricky enough on land, but in the ocean it’s an even harder proposition. Yet without knowledge of marine animal populations, conservation efforts can’t be directed effectively. One way to solve this issue is to examine drivers of site occupancy – what causes some populations to thrive or decline in an area. Understanding these drivers can allow researchers to predict population declines and gain insight into the probability of local population extinctions.

Sawfish are a family of rays with distinctive long, flat snouts which have horizontal teeth running along the length to resemble saws. Known as rostrums (an alternative definition to the more common meaning of a raised platform for speaking or performing from) they are packed with electroreceptors that allow them to detect prey, whilst the teeth are thought to be used in a swiping motion to incapacitate fish.

Sadly, three of the five sawfish species are Critically Endangered and the other two are Endangered. Since sawfish aren’t commonly sighted keeping track of their populations is hard and there’s little systematic monitoring. To address this Yan et al. (2021) combined data from occurrence surveys with indices of ecological carrying capacity, fishing pressure and management capacity to predict local population extinctions and identify regions where conservation efforts might be most effective.

Overfishing of sawfish is a particular threat: their fins are prized for shark fin soup (whilst sawfish are known as Carpenter sharks, they aren’t actually sharks), their teeth are used as spurs for cockfighting, their rostrum are frequently sold as novelties or trophies, and parts of them are used in traditional medicines in countries including China, Mexico, Brazil, India, Kenya and Iran.

Accidental overfishing is an issue too: their iconic rostrum and teeth are easily tangled in fishing nets and lines. What’s more, untangling sawfish from nets can be difficult and dangerous so some fishermen will kill them before bringing them aboard.

By understanding issues like overfishing and habitat loss Yan et al. were able to show that sawfish are likely to be extinct off the coasts of 55 of the 90 countries where they previously existed. Their findings also suggest that if eight nations prioritise sawfish conservation (Cube, Tanzania, Colombia, Madagascar, Panama, Brazil, Mexico and Sri Lanka), then up to 71.5% of the sawfish family’s historical global distribution would be protected.

Original research: https://doi.org/10.1126/sciadv.abb6026

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Hedgerow Snuffling by Roy McGhie

Hedgerow snuffling and
intensive farming practices.
A prickly issue.

By Roy McGhie

Hedgehog numbers are declining. Although hedgehogs are often thought of as a countryside animal, recent studies have shown that they are now most likely to be found in urban habitats in the UK.

A recent paper by Yarnell and Pettett (2020) has reviewed the difficulties they face in the rural environment (namely lack of food availability, habitat connectivity and shelter) and highlighted some of the agri-environment options from which they could benefit. However, there is a lack of empirical evidence around the precise benefits such options (like establishment of field margins and boosting hedgerow cover) would bring. More studies are urgently required before hedgehogs and other insectivores are driven out of the countryside entirely.

Original research: https://doi.org/10.3390/ani10091566

Roy McGhie works for Natural England as an Uplands Advisor. You can connect with him on LinkedIn here. If you enjoyed his sciku, check out his previous poems Ghost Ponds, A Heady Mixture and Fluttering by at Dusk.

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Wildfire’s Secrets

Hidden harm of smoke.
Microbial long-haul flights.
Lurking, infecting.

Wildfires cause huge amounts of long-term harm, including human, other animal and plant deaths, habitat loss, property and infrastructure destruction, the loss of carbon reservoirs and increased chances of flooding and landslides. Small airborne particles in smoke can be inhaled and cause fatal problems within the respiratory system, whilst the high levels of carbon monoxide produced can result in long-term brain damage, heart problems and even suffocation.

Yet researchers are revealing a new potential health threat as a result of wildfires – some microbes and fungi known to cause human infections are able to survive in the smoke plumes. Wildfires disturb soils causing these microbes to become airborne. Within the smoke the microbes ‘travel’ on particulate matter which is likely to protect them from ultraviolet radiation.

Kobziar & Thompson (2020) argue that the ability of microbes to survive in smoke plumes means that wildfires could play a role in geographical patterns of infection and that more research is needed to understand this threat. Particulate matter from wildfire smoke has been found to travel inter-continental distances. Those living close to wildfires, and even more so those firefighters working on the front lines are likely to be most at risk to such microbes – the US Centre for Disease Control has already stated that firefighting is an at-risk profession for coccidioidomycosis, a fungal infection also known as Valley fever.

The researchers argue that too little is currently known about microbe survival and spread in wildfire smoke. Essential questions remain, the answers to which will only be more important as the likelihood of wildfires increases as a result of climate change.

Original research: Kobziar & Thompson, 2020, Science, ‘Wildfire smoke, a potential infectious agent’ https://science.sciencemag.org/cgi/doi/10.1126/science.abe8116

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Diving for Science by Dr. Phil Colarusso

Collecting data
Breathing air underwater
They pay me for this!

By Phil Colarusso

The US Environmental Protection Agency (EPA) uses scuba diving as one of many tools to study and monitor aquatic systems.  EPA currently supports 65 divers spread throughout the United States. 

Divers are involved in a wide range of scientific pursuits, including studying, monitoring and restoring valuable aquatic habitats (coral reefs, seagrass meadows, shellfish beds), tracking invasive species, collecting sediment and water samples for chemical analysis and a wide range of other duties. 

Photo credit: Phil Colarusso

EPA divers go through a rigorous training program and are required to maintain high levels of diving proficiency and safety protocols.  For more information on EPA’s scientific diving program go to: https://www.epa.gov/diving

Dr. Phil Colarusso is a marine biologist with US EPA Region I.  He has been working on eelgrass restoration, conservation and research for 31 years.  He and his team just recently had a paper on carbon sequestration rates in eelgrass in New England accepted for publication.

Enjoyed Phil’s sciku? Check out his previous sciku Blue Carbon and Invasive Species.

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Technomancy by Debbie Lee

Fitbit in your skull,
neuroscience leap
Musk technomancy

by Debbie Lee

Neuralink is a brain implant with 1,024 5-micron-wide (very, very thin!) electrodes and includes sensors for motion, temperature and pressure. Ultimately, according to Elon Musk, the medical goal is for such implants to be able to control prosthetic limbs, alleviate memory loss, help with addiction and fix mental illnesses and vision and hearing impairments.

Musk has described it as “a Fitbit in your skull” and some of his more enthusiastic claims are that this technology could one-day record and replay memories and (due to the device’s wireless capabilities) enable telepathy – sending and receiving words, concepts and images.

All this sounds incredible and Neuralink is certainly a step up from what has currently been available to neuroscientists – the current Utah Array has 64 electrodes and installation can cause significant tissue damage on installation and removal.

Whilst Neuralink represents a huge step forward for neuroscientists, however, there are still plenty of unknowns to do with how neurons function and how this type of technology can remain in the brain for long periods of time without causing tissue damage or being damaged by the environment within the cranium and the human immune response. For all of Musk’s technomancy hype, Neuralink currently asks more questions than it provides answers to and there are still plenty of difficult barriers to overcome before any of the promised advantages are possible.

Further reading: https://www.wired.com/story/neuralink-is-impressive-tech-wrapped-in-musk-hype/

Debbie Lee (@lee_debbie):
Writing from places light and dark,
awkward data nerd,
elegant word nerd,
dreaming in colour,
clumsily balancing love, hope,
kindness with pragmatic realism.

Read more of Debbie’s sciku here!

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Cobwebs to Foodwebs by Dr. Jon Hare

collecting
fish stomach contents
from file cabinets

By Jon Hare

Field studies take a lot of effort. Think of studying fishes in an estuary – where a river meets the sea. You need the expertise to know the fishes and how to take the variety of biological samples including earbones, stomachs, and gonads. You need a boat and gear to catch fish of different sizes and habits. You need to be able to deal with weather, seasons, and the other elements of nature. You need a group of people with varying expertise committed to work together. You need funding for the project. And the field effort is just the beginning – samples need to be processed in the laboratory, data compiled and analyzed, the results published, and the data made available. Now think about how many field studies or parts of field studies never make it to those final steps of dissemination. What happens to these studies? What happens to all that effort? 

Hanson and Courtenay (2020) describe the fate of one such effort. A multi-year fish-related field program was undertaken from 1991 to 1993 to describe the structure and function of the Miramichi River and Estuary ecosystem in eastern Canada. After several years, the project ended owing to a change in priorities (and funding); the team of scientists and fishers went their separate ways. Some of the results were published – primarily around high profile species like Atlantic cod and Atlantic salmon. However, many of the samples and much of the data never made it to the dissemination stage of science. 

The study by Hanson and Courtenay is part of an effort to recover the large amounts of field data stored in old file cabinets, on floppy disks, and in unpublished theses. In their study, Hanson and Courtenay use data collected during the Miramichi Estuary program and present detailed descriptions of the stomach contents of more than 8,000 individual fish across a range of species. Through these analyses, they describe the seasonality in the estuary both in terms of fish occurrence and diet. They also identify a small shrimp species (Crangon septemspinosa – Seven-spined Bay Shrimp) as a keystone species, linking estuarine and coastal foodwebs. Although the findings are not earth-shattering, the results and data are now available for future studies, which could model foodweb dynamics in the ecosystem (e.g. using EcoPath) or document ecosystem changes over the past three decades (a neat example from Long Island Sound, USA). Field studies and the subsequent research based on field studies are essential to developing strategies for ecosystem resilience and climate adaptation and ultimately for living sustainably within the earth system. 

Original research: Hanson, J. M., & Courtenay, S. C. (2020). Data Recovery from Old Filing Cabinets: Seasonal Diets of the Most Common Demersal Fishes in the Miramichi River Estuary (Atlantic Canada), 1991–1993. Northeastern Naturalist, 27(3), 401-433. https://doi.org/10.1656/045.027.0302

Dr. Jon Hare is a scientist who works in Woods Hole, Massachusetts. His research background is fisheries oceanography and climate change impacts on marine fisheries. Check out Jon’s other sciku ‘Owls of the Eastern Ice’, ‘Varves’, ‘Signs of Spring’ and ‘Glacier Mice‘.

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Invasive Species by Dr Phil Colarusso

Misplaced visitors
Cryptic hitchhikers on boats
Food webs are altered

By Phil Colarusso

While doing eelgrass restoration work in Gloucester, I became aware of a bluish-gray growth appearing on a large number of shoots. Shortly thereafter, I read in the Woods Hole journal Oceanus about a researcher who was seeing a new species of invasive tunicates (Diplosoma listeria) appearing on scallops, boat hulls, mooring lines and eelgrass on Martha’s Vineyard. The photo was of exactly the same thing I was seeing in Gloucester.

Tunicates are filter feeding organisms that can grow as small zooids in extensive colonies or as large solitary individuals. The colonial forms tend to be prolific breeders and filter enormous quantities of water. They can grow quickly and will cover just about any surface that is bare, including pilings, clam shells, algae and eelgrass. Recent research has shown that literally miles of the seafloor can be covered by one of these colonial species, smothering other sessile life and altering the availability of the habitat.

Photo credit: Phil Colarusso

My team decided to conduct a study in a salt pond on Martha’s Vineyard, where these organisms had appeared to be particularly abundant. We initially had focused on the impact of these animals to the eelgrass in the pond, but quickly realized their prolific filter feeding may pose an additional risk to the food web of this small coastal pond.

Using stable isotopes, we determined the tunicates were feeding on the same resources as several commercially important shellfish species. Based on their high abundance, their prolific feeding rates and the small volume of the pond, our modelling suggested the tunicates could potentially filter a volume of water equivalent to the entire pond in somewhere between 1 and 17 hours. This represents a significant challenge for commercial shellfish stocks in these waters. You can see a video on this project here.

Photo credit: Phil Colarusso

It is not always clear where and how these invaders arrive, but shipping is believed to be a major vector. Planktonic life forms and small creatures are carried in ballast water and along the hulls or larger vessels. Globalization has significantly increased shipping all over the planet and as a result the unintentional transportation of organisms as well. Early detection may allow for some level of control, but often once a new species is detected in the ocean, control options are untenable. Persistent monitoring is the most prudent tool in identifying and controlling the spread of non-native species.

Original research:

Colarusso, P. et al. (2016) Quantifying the ecological impact of invasive tunicates to shallow coastal water systems. http://dx.doi.org/10.3391/mbi.2016.7.1.05

Valentine, P.C. et al. (2007) The occurrence of the colonial ascidian Didemnum sp. on Georges Bank gravel habitat – Ecological observations and potential effects on groundfish and scallop fisheries. https://doi.org/10.1016/j.jembe.2006.10.038

Dr. Phil Colarusso is a marine biologist with US EPA Region I.  He has been working on eelgrass restoration, conservation and research for 31 years.  He and his team just recently had a paper on carbon sequestration rates in eelgrass in New England accepted for publication.

Enjoyed Phil’s sciku? Check out his other of his sciku Blue Carbon and Diving for Science.

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Signs of Spring by Dr. Jon Hare

silvery white
shadbush blossoms
swim upstream

By Jon Hare

Shadbush (Amelanchier arborea) blooms in the spring. Clusters of small white flowers appear in March through May before leaves grow. The bloom time coincides with the upstream migration of American shad (Alosa sapidissima). Millions of shad used to return to east coast rivers, but these runs are now greatly reduced because of historical overfishing, dams, and loss of habitat.

Much like salmon, shad return to rivers to reproduce after several years at sea. Unlike salmon that reproduce and die, shad go back to sea after reproducing to return to rivers in following years to reproduce again. Thus salmon are termed semelparous from the Latin semel – once, a single time. Shad are termed iteroparous from the Latin itero – to repeat.

Photo credit: NOAA Fisheries Northeast Fisheries Center.

Shadbush is also iteroparous – blooming year after year in the spring to mark the return of the shad. Recent research by Nack et al. (2019) indicates shad migration will be earlier in the season; whether shadbush will bloom earlier remains to be seen.

Original research: https://doi.org/10.1002/mcf2.10076

Dr. Jon Hare is a scientist who works Woods Hole, Massachusetts. His research background is in fisheries oceanography and climate change impacts on marine fisheries. Check out Jon’s other sciku ‘Owls of the Eastern Ice’, ‘Varves’, ‘Cobwebs to Foodwebs’ and ‘Glacier Mice‘.

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Blue Carbon by Dr. Phil Colarusso

Climate change buffer
Particles settle in grass
Seagrass meadows rule

By Phil Colarusso

Seagrass meadows collect and sequester large amounts of carbon in the sediments below the meadows.  The carbon accumulates through 2 different pathways.  First, through photosynthesis and tissue growth, seagrasses extract carbon from the water column and incorporate it into its own tissues. The root and rhizome structures and some cast leaf material end up being incorporated into the sediments.  In most cases, this provides less than half of the carbon found in those sediments.  The majority of the carbon in the sediments originates from outside of the meadow.  The canopy of the meadow functions as a filter, facilitating the settlement of organic particles as the tide passes over the meadow going in and out. 

As long as the meadow stays intact, the carbon in the sediments remains isolated and out of the global carbon cycle.  Data shows that the age of carbon in meadows can be hundreds of years old.  Seagrass meadows, salt marsh and mangroves all perform the same carbon sequestration function and collectively are referred to as blue carbon habitats.  This is still a relatively young field of research.

Photo credit: Phil Colarusso

In the above photo, you can see the seafloor in the foreground, which is primarily sandy cobble.  The eelgrass meadow has a dark organic layer indicating the large carbon component that has accumulated due to the presence of the plants.

Further reading on seagrass blue carbon: https://doi.org/10.1038/ngeo1477

Dr. Phil Colarusso is a marine biologist with US EPA Region I.  He has been working on eelgrass restoration, conservation and research for 31 years.  He and his team just recently had a paper on carbon sequestration rates in eelgrass in New England accepted for publication.

Interested in seagrass meadows? They’re also hugely important for the world’s fisheries. Find out more in the sciku Forgotten Value here. You can also check out Phil’s sciku Invasive Species and Diving for Science.

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Backlit Billboards in the Sea by Prof Teena Carroll

Sending messages,

luminescent Humboldt Squid

flicker in the deep.

by Teena Carroll

A group of scientists at the Monterey Bay Aquarium Research Institute conducted a study of Humboldt squid using remote operated vehicles.  They wanted to determine how a group of squid could execute complex behaviors in low light deep sea conditions.  For instance, the squid avoid body contact with each other even when pursuing the same prey.

Burford and Robison (2020) found that the squid used specific color patterns on their bodies primarily when they were hunting in groups.  Normally, such color changes would not be visible in the deep sea; Humboldt squid are bioluminescent which researchers hypothesize essentially provides backlighting to highlight the color changes.

The complexity of the color changes prevented the researchers from translating exactly what the squid are communicating.  However they were able to document that the patterns are a consistent and effective communication method.  After observing repeated patterns, they think that the visual language of the squid may be evolved enough to use syntax.

Original research: https://doi.org/10.1073/pnas.1920875117

Additional information: https://www.mbari.org/humboldt-squid-signaling/

Teena Carroll is a mathematics professor at Emory & Henry College in Southwest Virginia and has been a poet longer than she has been a mathematician. @Teena Carroll