Archive for the ‘Bioenergy’ Category

February 28, 2023

New predictive models developed for bacterial diversity of soils

by Joslyn Neiderer, Pennsylvania State University Credit: Pixabay/CC0 Public Domain

A new set of quantitative models that incorporates pH into the metabolic theory of ecology (MTE) has been developed by an international team that includes Penn State assistant professor of plant science Francisco Dini-Andreote.

The work is included in a new paper published by the Proceedings of the National Academy of Sciences, titled, “Integrating pH into the metabolic theory of ecology to predict bacterial diversity in soil.”

“Soils are the most complex and biodiverse ecosystems on Earth,” said Dini-Andreote, a member of Penn State’s Microbiome Center. “In soils, microbial diversity plays indispensable roles in the anabolic and catabolic cycles of carbon, nitrogen and sulfur, without which the diversity of life forms—including plants, animals and other microbes—that evolved on our planet would not have been possible. In addition, advancing our ability to predict patterns of soil biodiversity is critical to better understanding how climate change will affect soil functioning and how soil microbes will respond to shifts in temperature and precipitation regimes.”

In general terms, the metabolic theory of ecology links rates of organism diversification (i.e., the metabolic rate of an organism) with the organisms’ body size and body temperature, explained Dini-Andreote. Building upon the factors that are parametrized in the MTE, the researchers introduced variation in local pH as an additional variable that acts as a stringent selective filter of biodiversity in soils, impacting the species of microbes acting and surviving in the soil.

By considering all these factors—the metabolic rate, mass, and temperature as well as pH—the researchers were able to capture and account for previously unexplained variation in the relationship between soil edaphic properties (the physical, chemical, and biological properties of the soil), temperature, and biogeographical patterns of bacterial diversity. The team then continued to test and validate their models across multiple scales—such as single bacterial strain diversification rates, local and continental scale soil communities—yielding robust results.

“By layering these models, researchers can start to better understand patterns of microbial distribution in soils and start to answer long-standing questions in this field, such as: ‘What determines variation in soil biodiversity?’ and “How dynamic changes in soil biodiversity can be modeled and predicted?” said Dini-Andreote.

“With that, we will be able to better harness the genomic and functional potential of these soil microorganisms to effectively manipulate them for desirable outcomes. These outcomes vary from essential ecosystem functions, such as carbon storage in soil, to the manipulation of beneficial plant-associated microorganisms to enhance crop productivity in agriculture.”

This study also represents a nexus point for the integration of other variables into these quantitative models, such as variation in soil moisture and salinity, among others. The authors foresee new avenues of research ahead that will greatly improve scientists’ ability to understand the distribution of soil microbial species, and the diverse ways they operate as engineers of essential ecosystem processes and services in soils.

“Dr. Dini-Andreote’s scholarship shines a bright light on the abundance of the soil microbiome and the processes and mechanisms that shape soil health. From the soil on up, microbial communities connect different ecosystems as microorganisms flow from soil to hosts and back. With soil as the largest reservoir of microbial diversity on Earth, this important work raises the call to action as soils vary and degrade due to climate change, erosion, and chemical contamination,” said Seth Bordenstein, director of the Penn State Microbiome Center, Dorothy Foehr Huck and J. Lloyd Huck Chair in Microbiome Sciences, professor of biology and entomology.

More information: Lu Luan et al, Integrating pH into the metabolic theory of ecology to predict bacterial diversity in soil, Proceedings of the National Academy of Sciences (2023). DOI: 10.1073/pnas.2207832120

Journal information: Proceedings of the National Academy of Sciences

Provided by Pennsylvania State University

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JAKARTA] Rapid cropland expansion is the main cause of biodiversity loss in tropical countries, a study by UNEP’s (the UN Environment Programme) World Conservation Monitoring Centre and the Cambridge Conservation Initiative has found.

The study, published in PLOS ONE last month (9 January), highlights maize and soybean as the most expansive crops and as the main drivers of biodiversity loss in tropical regions. Other crops that pose a major threat to habitats and wildlife are beans, cassava, cowpea, groundnut, millet, oil palm, rice, sorghum, sugarcane and wheat, the study says.


  • Rapid expansion of crops such as maize and soybean is leading to biodiversity loss in tropical countries
  • Researchers say pace of expansion could derail progress towards meeting the Aichi Biodiversity Targets
  • A range of sustainability standards and policies are suggested as a way forward

It estimates that cropland in tropical countries expanded by 48,000 square kilometres per year from 1999 to 2008, with Brazil, Ethiopia, Indonesia, Nigeria and Sudan experiencing the greatest expansion.

Stuart H. M. Butchart, a UNEP researcher and one of the authors of the study, tells SciDev.Net: “Unsustainable agriculture is the most significant threat to biodiversity, but conservationists have not previously paid much attention to quantifying which particular crops have caused the greatest problems, nor which ones may do so in the future. This [study] starts to address this issue”.

One example of crop expansion cited in the study that has quickened the rate of species extinction is the Mega Rice Project in Kalimantan, Indonesia. Vast tracts of peat swamps were drained starting from the late 1990s in misguided attempts to turn them into rice plantations.

More than one million hectares, an area about a third the size of Belgium, have been converted for rice production, threatening the survival of Borneo’s last orangutans.

Similarly, peat and forest areas gave way to oil palm in Indonesia and Malaysia while soybean expansion have also replaced habitats of particularly high biodiversity value in the Brazilian Cerrado savanna. Expanding maize cultivation also threatens the dry forests of Madagascar.

Krystof Obidzinski, a scientist at the Centre for International Forestry Research, in Bogor, Indonesia, says that large-scale land acquisition is proceeding apace in countries like Indonesia — with economic benefits dominating the agenda while environmental impacts appear to be underestimated.

If the pace of expansion continues, the report warns, it could derail progress towards meeting the Aichi Biodiversity Targets, a set of 20, time-bound measurable targets aimed at halting global biodiversity loss by the middle of the century.

Butchart believes there should be a system in place so that consumers can make informed choices about the food they buy and how sustainably they have been produced. Such a system could reduce and minimise impacts of agriculture on biodiversity.

Customers can then discern which products are least damaging to the environment and producers have an incentive to minimise their negative impacts.

The study highlights the urgent need for more effective sustainability standards and policies addressing both production and consumption of commodities including robust land-use planning in agricultural frontiers, establishment of new protected areas or REDD+ projects in places agriculture has not yet reached, and reduction or elimination of incentives for land-demanding bioenergy feedstocks.

This article has been produced by SciDev.Net’s South-East Asia & Pacific desk.

Link to full article in PLOS ONE



PLOS ONE doi:10.1371/journal.pone.0051759 (2013)



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Wisconsin State Farmer

April 8, 2014 12:37 p.m.


Invasive Plant Science and Management — Cultivation of large grasses for bioenergy production is gaining interest as a renewable fuel source. A sterile hybrid, giant miscanthus, is a promising bioenergy crop that, unfortunately, carries a high establishment cost for growers. A new seed-bearing line may have economic benefits, but it also bears consequences as an invasive species if it escapes cultivation.

The article “The Relative Risk of Invasion: Evaluation of Miscanthus × giganteus Seed Establishment,” reports the results of field tests on the fertile “PowerCrane” line of giant miscanthus. There is a dearth of research on the ability of such newly developed fertile crops to escape cultivation. Such research can identify susceptible habitats and help advance management plans in preparation for widespread commercialization.

Giant miscanthus produces abundant biomass, has few pests, and requires few inputs after establishment. While these traits make it an excellent bioenergy crop, they are also traits of invasive species. This species has the ability to produce up to 1 billion spikelets per acre per year that can disperse seed into the wind.

In this study, seedling establishment was evaluated in seven habitats: no-till agricultural field, agricultural field edge, forest understory, forest edge, water’s edge, pasture, and roadside. Experiments were conducted at three sites in the southeastern United States —the area most likely to see increased bioenergy production due to its ideal growing conditions.

Giant miscanthus seedlings emerged in roadside and forest edge habitats at all study sites, and early in the growing season, there were more giant miscanthus seedlings in the agricultural field than any of the other species.Despite its potential, in these tests giant miscanthus experienced high seedling mortality — 99.9 percent overall.

However, identification of even a small population of an escaped species at an early stage can be critical for effective eradication. A 99.9 percent mortality rate in spikelets per acre leaves 1 million spikelets in the seed bank.

This study looks at the early establishment phase of invasion, which is only part of the process. With growing demand and federal mandates, bioenergy production is on the increase, and evaluation of these crops’ potential as invasive species will be essential for management.

Full text of the article “The Relative Risk of Invasion: Evaluation of Miscanthus × giganteus Seed Establishment,” Invasive Plant Science and Management, Vol. 7, No. 1, January-March 2014, is now available.


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