Category Archives: biodiversity

How to Engineer Bacteria to Search for Underground Chemical Weapons: DARPA

U.S. military researchers asked in 2019 two companies to develop new kinds of biological sensors that can detect underground disturbances or the presence of buried chemicals or weapons.

Officials of the U.S. Defense Advanced Research Projects Agency (DARPA) in Arlington, Va., are looking to Raytheon BBN Technologies, and Signature Science, for the BioReporters for Subterranean Surveillance program.  This project seeks to use indigenous and engineered organisms to sense changes of interest to military commanders in natural and built environments. Raytheon BBN and Signature Science won separate $1.6 million contracts for the Subterranean Surveillance progam.

The two companies will perform laboratory research and proof-of-concept demonstrations of biological sensing systems in well- controlled field tests that take advantage of recent advances in microbial science and synthetic biology to develop biological sensors, signal transducers, and reporters that can reveal subterranean phenomena at a distance.  Bio Reporters should be able to sense a phenomenon at least one meter below the surface, propagate a signal to the surface within seven days, and be continuously detectable on the surface at a distance of 10 meters over the subsequent seven days.

DARPA researchers want Raytheon BBN and Signature Science experts to take advantage of the extensive biological networks that exist underground to monitor large areas to increase the military’s ability to detect subterranean events without the need for precise coordinates.

Excerpts from John Keller, Researchers eye new biological sensors to to detect underground objects like buried chemicals and weapons, https://www.militaryaerospace.com,  Nov. 6, 2019

In more detail  Signature Science and its partner, the Texas A&M University Center for Phage Technology, aim to leverage modern and synthetic phage biology and the straightforward molecular genetics of the harmless soil bacterium Bacillus subtilis to generate a new platform to recognize and report on specific chemical threats underground. The Spore-Phage Amplified Detection (SPADe) method, potentially extensible to explosives, radiation or physical disturbance sensing, seeks to substantially advance currently used techniques which rely heavily on manual soil testing. 

When Logging Works: “Every Part of the Tree”

The rapacious industrialisation of the Finnish forest, which covers three-quarters of the country’s landscape, looks the antithesis of tree-hugging environmentalism. The forest is home to wolves, bears, deer and many other species of wildlife, and its trees lock away carbon that would otherwise be in the air, warming the atmosphere. Yet Metsä Group, which operates the Äänekoski pulp mill, claims the very opposite.  Metsä is ultimately controlled by a co-operative belonging to more than 100,000 families who have each owned large chunks of the forest for generations. For every tree harvested, four saplings are planted. These are allowed to grow for a few years and are then thinned to encourage the best specimens to develop vigorously. The thinnings, however, are not wasted. They are sent to the mill. The mature trees, meanwhile, are harvested when they are between six and ten decades old. The consequence of this husbandry, according to Finland’s Natural Resources Institute, is that the annual growth of trees in Finland exceeds the volume of felling and natural loss by over 20m cubic metres, despite the increasing demand for wood.

As for the mill itself, Metsä’s stated aim is to make best use of every part of a tree, both to maximise the value of its wood and, where possible, to continue to lock up its carbon. To this end, besides the bread-and-butter business of turning out planks and plywood, the firm has come up with several new ideas. Three are of particular interest. One is a better way of converting wood pulp into fibre that can be turned into textiles. A second is to produce plastic-free cardboard cartons which can be used as food containers and then recycled. The third is to find employment for lignin, a by-product of the pulping process which is, at the moment, usually burned…

Metsä has also teamed up with Itochu, a Japanese trading company with a large clothing business, to make fabric that will compete with oil-based synthetic fibres and provide an alternative to cotton, the growing of which requires a lot of land, irrigation and pesticides. Some fabrics—rayon, for example—can be made from wood….

The complex processes involved in processing wood result in several “sidestreams”. These are wastes that become raw materials for other processes. They include sulphuric acid, which is re-used by the mill, and biogas, tall oil (a byproduct of papermaking) and lignin—carbon-rich materials burnt to produce electricity. This powers the mill, and yields a surplus which is exported to the national grid. As a consequence, unlike some wood mills, the Äänekoski plant uses no fossil fuels.

Excerpts from Sustainable Forestry: If you go down to the woods today, Economist, Oct. 19, at 75

Bio-Energy and Food Security

In the effort to keep the planet from reaching dangerous temperatures, a hybrid approach called BECCS (bioenergy with carbon capture and storage) has a seductive appeal. Crops suck carbon dioxide (CO2) from the atmosphere, power plants burn the biomass to generate electricity, and the emissions are captured in a smokestack and pumped underground for long-term storage. Energy is generated even as CO2 is removed: an irresistible win-win. But, the United Nations’s climate panel sounded a warning about creating vast bioenergy plantations, which could jeopardize food production, water supplies, and land rights for poor farmers.

In an earlier special report in October 2018, IPCC called for holding the rise in global average temperatures to no more than 1.5°C above preindustrial conditions to avoid the worst consequences of climate change. It emphasized that cutting emissions won’t be enough to reach that goal. Replacing coal with renewable energy, and significantly cutting oil and natural gas, would still leave gigatons of excess carbon in the atmosphere. BECCS could remove it, computer models suggested, if several million square kilometers—an area the size of India—were devoted to energy crops.

But the 2019 IPCC report examines the consequences of deploying BECCS on that vast scale and concludes it could “greatly increase” the demand for agricultural land. The pressure on conventional crops could compromise food security, as happened in 2007 when rising U.S. corn ethanol production contributed to a spike in food prices. (In Mexico, the price of tortillas, a staple for the poor, rose 69% between 2005 and 2011.) The bioenergy plantations could also take a toll on biodiversity—as is happening in Southeast Asia, where plantations producing palm oil for biodiesel as well as food are displacing diverse tropical forest. And they could suck up scarce water, especially in drylands, where irrigation of crops might deplete local supplies, the IPCC report says.

Industrial bioenergy crops can lead to the same kinds of problems as intensive food production, such as the contamination of water from excess fertilizer. Scaling up bioenergy in developing countries can also exacerbate social problems like the loss of land by small farmers.

Excerpts from Erik Stokstad, Bioenergy plantations could fight climate change—but threaten food crops, U.N. panel warns, Science, Aug. 8, 2019

The Disappearing Birds

North America’s birds are disappearing from the skies at a rate that’s shocking even to ornithologists. Since the 1970s, the continent has lost 3 billion birds, nearly 30% of the total, and even common birds such as sparrows and blackbirds are in decline, U.S. and Canadian researchers reported in the September 2019 Issue of Science Magazine…  Five  years ago, PM Rosenberg a conservation biologist decided to take a broader look at what is happening in North America’s skies.

“I frankly thought it was going to be kind of a wash,” Rosenberg says. He expected rarer species would be disappearing but common species would be on the rise, compensating for the losses, because they tend to be generalists, and more resilient. Indeed, waterfowl and raptors are thriving, thanks to habitat restoration and other conservation efforts. But the declines in many other species, particularly those living along shorelines and in grasslands, far exceeded those gains, Rosenberg and his colleagues report. Grassland birds have declined by 53% since 1970—a loss of 700 million adults in the 31 species studied, including meadowlarks and northern bobwhites. Shorebirds such as sanderlings and plovers are down by about one-third, the team says. Habitat loss may be to blame.

The familiar birds that flock by the thousands in suburbs were not exempt. “There’s an erosion of the numbers of common birds,” Rosenberg says. His team determined that 19 common species have each lost more than 50 million birds since 1970. Twelve groups, including sparrows, warblers, finches, and blackbirds, were particularly hard hit. Even introduced species that have thrived in North America, such as starlings and house sparrows, are losing ground.  “When you lose a common species, the impact will be much more massive on the ecosystem and ecosystem services,” says Gerardo Ceballos, an ecologist and conservation biologist at the National Autonomous University of Mexico in Mexico City. “It’s showing the magnitude of the problem.”

Some of the causes may be subtle. Last week, toxicologists described how low doses of neonicotinoids—a common pesticide—made migrating sparrows lose weight and delay their migration, which hurts their chances of surviving and reproducing. Climate change, habitat loss, shifts in food webs, and even cats may all be adding to the problem, and not just for birds. 

Weather radar data revealed similarly steep declines. Radar detects not just rain, but also insect swarms and flocks of birds, which stand out at night, when birds usually migrate. “We don’t see individual birds, it’s more like a big blob moving through airspace,” explains Cornell migration ecologist Adriaan Dokter. He converted “blobs” from 143 radar stations into biomass. Between 2007 and 2017, that biomass declined 13%, the Science paper reports. The greatest decline was in birds migrating up the eastern United States….

Excerpts from Elizabeth Pennisi, Billions of North American Birds Have Vanished,  Science, Sept. 20, 2019

A Cure Worse than the Disease? Biofuels in Planes

The 2019 report by the Rainforest Foundation Norway RFN is called ‘Destination Deforestation’ and reviewed the role of the aviation industry in contributing to the climate crisis, concluding that there’s a high risk that increased use of palm and soy-based biofuel in planes will lead to increased deforestation.

Finland, the world’s largest producers of renewable diesel and the only EU country that gives additional incentives for the use of palm oil products to manufacture biofuel, could spearhead the race towards deforestation, as areas of rainforest in countries like Indonesia or in South America are cleared to plant crops that will later be used to produce the fuel.  RFN says that meeting the aviation industry’s own climate-change targets to reduce emissions could result in 3.2 million hectares of tropical forest lost, an area larger than Belgium.

Researchers at Rainforest Foundation Norway believe the Finnish incentives for (Palm Fatty Acid Distillate) PFAD-based biofuels are likely to contribute to this deforestation, since Finland’s state-owned oil company Neste produces half of the world’s renewable diesel.  “Finland continues to treat the palm oil by-product PFAD as a waste, eligible for additional incentives. In addition, Finland is home to Neste, the world’s largest producer of hydrotreated biodiesel, and uses PFAD as a raw material. Therefore, Finland’s program could contribute to the massive deforestation discussed in our report” he explains.

With Finland left isolated as the only EU country to pay producers to use waste-classified PFAD in biofuel production, Rainforest Foundation Norway cautions that the country risks becoming a dumping ground for unsustainable raw material….“As long as PFAD is classified as ‘waste’, it enjoys huge incentives from the state. Biofuels made out of PFAD are completely exempt from carbon dioxide tax in Finland. Additionally, PFAD’s emissions can be discounted, and it is not subject to the same sustainability criteria as other raw materials.

With ‘flight shame’ gaining more momentum across the world, the aviation industry is desperate to find ways to make flying compatible with climate goals. While replacing fossil fuels with renewables sounds like a great idea, the sustainability of biofuels is highly dependent on the raw materials used to produce them…The most common aviation biofuels, Hydrogenated Esters and Fatty Acids (HEFA) fuels are produced from vegetable oils and animal fats. While the use of waste oils and other recycled materials is possible, the most viable raw materials for HEFA jet fuels are food crops.  “The cheapest and most readily available raw materials for HEFA jet fuel are palm oil and soy oil, which are closely linked to tropical deforestation” Ranum says.  The experts suggest that aiming to reduce emissions by increasing demand for palm and soy oil is a cure worse than the disease.

Elias Huuhtan, Report: Finland’s push to use biofuel could cause ‘massive deforestation, https://newsnowfinland.fi/ , Oct. 7, 2019

The Fight Against Toxic Algae

Signs posted around the Grand Lake, Ohio read: “Danger: Avoid all contact with the water.”  When dangerously high levels of toxins from blue-green algae in Grand Lake, Ohiio were publicized in 2009, many residents and tourists stopped using the 13,000-acre lake in northwest Ohio. Hotel revenue and home values sank for several years as algae bloomed in the state’s largest inland lake.

Greenish water still laps at Grand Lake’s shores, but recent water samples show that the amount of algae-feeding nutrients entering the lake is down significantly. State, federal and private donations covered more than $10 million in projects aimed at improving water quality. More people are boating on the lake again. Grand Lake could now serve as an example for communities with algae problems across the nation, experts say.

Algal blooms are on the rise, from Lake Erie to the Florida Everglades. In August 2019, the Environmental Protection Agency listed algae-related beach closures or health advisories in 23 states, and it said other blooms may not have been reported. In 2010, the EPA found that 20% of 50,000 lakes surveyed had been affected by phosphorous and nitrogen pollution, which feeds algae.e  Cleaning up bodies of water choked with toxic algae has proved difficult. The project to repair Grand Lake, once one of the most polluted by algae in the nation, is one of the clearest successes. It shows cleanup is possible, but also expensive and time-consuming.

“It’s not restored yet, but it’s on the road to recovery,” said Stephen Jacquemin, an associate professor of biology at Wright State University-Lake Campus in Celina.  Beginning in 2012, wetlands areas were built around the lake, which was hand dug in the 1830s. The thick stands of bulrushes and other plants have reduced phosphorous and nitrogen levels in water entering the wetlands before reaching the lake by as much as 90%, Dr. Jacquemin said.  Three wetland areas, which cost a total of about $6 million to build, are constructed as a series of interconnected pools that allow particulates to settle out and plants and microbes to remove nutrients.

Areal View of Artificial Wetlands, Great Lake Ohio

 The state’s Department of Natural Resources has also dredged the lake bottom to remove nutrient-loaded sediment, and tried to clean up one of Grand Lake’s beaches near St. Marys by building a rock jetty and installing aerators and a curtain to filter water. Recent water tests there showed levels below 6 parts per billion of the toxin microcystin, under Ohio’s threshold of 20 parts per billion for avoiding contact with water.

As Green Algae Forces Beaches to Close, Ohio Lake Offers Hope, WSJ, Sept. 18, 2019

The Truth About Forest Fires

BBC has used satellite data to assess the severity of fires in Brazil, Indonesia, Siberia and Central Africa.  It has concluded that although fires in 2019 have wrought significant damage to the environment, they have been worse in the past.   More than 35,000 fires have been detected so far in 2019 in East Asia  spreading smoky haze to Malaysia, Singapore, the south of Thailand and the Philippines, causing a significant deterioration in air quality.  But this is substantially fewer than many other years including those, such as 2015, exacerbated by the El Nino effect which brought unusually dry weather.

Haze Pollution

In Indonesia, peatland is set alight by corporations and small-scale farmers to clear land for palm oil, pulp and paper plantations, and can spread into protected forested areas.  The problem has accelerated in recent years as more land has been cleared for expanding plantations for the lucrative palm oil trade.  Old palm trees on plantations that no longer bear fruit are often set on fire to be replaced by younger ones.

The number of recorded fires in Brazil rose significantly in 2019, but there were more in most years in the period 2002 to 2010.  There is a similar pattern for other areas of Brazilian forestry that are not part of the Amazon basin.  For 2019, we have data up to the end of August, and the overall area burnt for those eight months is 45,000 sq km. This has already surpassed all the area burnt in 2018, but appears unlikely to reach the peaks seen in the previous decade… “Fire signals an end of the deforestation process,” says Dr Michelle Kalamandeen, a tropical ecologist on the Amazon rainforest.  “Those large giant rainforest trees that we often associate with the Amazon are chopped down, left to dry and then fire is used as a tool for clearing the land to prepare for pasture, crops or even illegal mining.”

The environmental campaign group Greenpeace has called the fires that have engulfed the Russian region of Siberia this year one of the worst outbreaks this century.  The cloud of smoke generated was reported to have been the size of all the European Union countries combined.  Forest fires in Siberia are common in the summer, but record-breaking temperatures and strong winds have made the situation particularly bad.  Russia’s Federal Forestry Agency says more than 10 million hectares (100,000 sq km) have been affected since the start of 2019, already exceeding the total of 8.6 million for the whole of 2018…. Drawing on data for the number of fires, it is clear that there have been other bad years, notably in 2003.

Nasa satellites have identified thousands of fires in Angola, Zambia and DR Congo.However, these have not reached record levels.  “I don’t think there’s any evidence that the fires we’re seeing in Africa are worse than we’ve seen in recent years,” Denis McClean, of the UN Disaster Risk Reduction agency, told the BBC.  According to data analysed by Global Forest Watch, fires in DR Congo and Zambia are just above average for the season but have been higher in past years.  In Angola, however, fires have been reported at close to record levels this year.

Some have drawn comparisons with the situation in the Amazon, but the fires in sub-Saharan Africa are different.  Take DR Congo – most fires are being recorded in settled parts of the country’s southern, drier forest and savannah areas, and so far not in tropical rainforest.  Experts say it is difficult to know what is causing these fires, which are seasonal. Many are likely to be on grassland, woodland or savannah in poor farming communities.  “Fires are very important landscape management tools and are used to clear land for planting crops,” says Lauren Williams, a specialist in Central and West African forests at the World Resources Institute.

Excerpts from Jack Goodman & Olga RobinsonIndonesia haze: Are forest fires as bad as they seem?, BBC, Sept. 19, 2019. For more details and data see BBC