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NEWS AND VIEWS
25 August 2021

African tropical montane forests store more carbon than was thought

The inaccessibility of African montane forests has hindered efforts to quantify the carbon stored by these ecosystems. A remarkable survey fills this knowledge gap, and highlights the need to preserve such forests.

Nicolas Barbier

0

Nicolas Barbier

Nicolas Barbier is at AMAP, Université de Montpellier, IRD, CNRS, INRAE, CIRAD, Montpellier 34980, France.

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In a paper in Nature, Cuni-Sanchez et al.1 report the assembly of a large database of tree inventories for 226 mature montane-forest plots in 12 African countries. The authors analyse the data to determine the amount of aboveground biomass and carbon stored in these highly diverse and threatened ecosystems. Their results suggest that African montane forests store more carbon than was previously thought, and the findings should help to guide efforts to conserve these ecosystems.Cuni-Sanchez and colleagues measured trunk diameters and heights of the trees in plots, and identified the botanical species to deduce wood density — an approach that constitutes the gold standard for estimating the biomass, and thus the amount of carbon, contained per unit of forest area. This method involves the use of general statistical equations for describing tree form, called allometric models, and considers only the aboveground parts of trees. It therefore disregards several other pools of carbon, notably in the roots and soil. The overall approach might seem crude, but recognizing and measuring the many hundreds of tree species found on steep, cloud-shrouded slopes (Fig. 1), let alone the underground carbon, without visiting the sites, will long remain difficult, even with the best drones and satellite systems.

Figure 1 | Montane forest in Boginda, Ethiopia. Cuni-Sanchez et al.1 use data from a survey of montane tropical forests in Africa to quantify the amount of carbon stored above ground in these ecosystems.Credit: Bruno D’Amicis/Nature Picture Library

Anyone who has conducted field inventories in tropical mountains knows that measuring and identifying 72,336 trees, often just a few steps away from the void, is an amazing feat. For comparison, a previously reported study2 based its estimates of the carbon stored in montane African forests on as few as seven plots. The study also brings together contributions from numerous researchers and institutions, including many in Africa, to greatly increase the size of the data set, which is also a remarkable achievement. Even so, the total area of forest studied is less than 150 hectares, whereas African montane forest covers about 100,000 times that area, inevitably raising questions about how representative the inventory is.Statisticians might raise their eyebrows at the sampling design. As is usually the case in meta-analyses, the data set was neither homogeneous (for example, there is a roughly tenfold variation in the plot sizes), nor were the sites selected at random. However, the authors did their best to rule out possible biases induced by sampling artefacts.
Read the paper: High aboveground carbon stock of African tropical montane forests
Cuni-Sanchez et al. chose not to discuss one tricky aspect of surveys of this sort (extensively discussed elsewhere2): how should the land area of a steep slope be measured? The authors followed standard practice, which is to measure the extent of forest plots and of land-cover types in reference to horizontal, planimetric areas (that is, the areas that would be represented on a 2D map, as if seen from the air). This tends to overestimate aboveground carbon because the sloped surface area is greater than that of the planimetric area — which means that the tree density of the planimetric area is higher than it is on the slope. By contrast, the use of planimetric areas underestimates total montane-forest area (by about 40%; see ref. 2). These two biases should roughly cancel each other out when estimating carbon stocks, or changes to stocks, for a region or country. But care should be taken not to combine data acquired using planimetric and non-planimetric areas in future meta-analyses, because the resulting estimates could end up well off the mark.One might expect that trees in mature African montane forests would be, on average, shorter — and therefore store less carbon — than their lowland counterparts, because of their lower environmental temperatures and shallow soils, frequent landslides and strong winds. However, this is not what Cuni-Sanchez et al. report. Instead, they find that average aboveground carbon stocks are not significantly different from those of mature lowland forests. This contrasts with the situation in the neotropics and southeast Asia, where montane forests store, on average, less carbon than do lowland forests.However, the new results fit with the 2016 discovery that the tallest African trees (81.5 metres) grow on Mount Kilimanjaro3, the highest mountain in Africa. African forests, in general, tend to contain fewer but larger-statured tree stands than does, for example, Amazonia4. The current study confirms that this peculiarity applies even at high altitudes.The authors investigate several possible drivers for the variations in biomass observed at different sites in their study, including topography, climate, landslide hazard, and even the presence of elephants or certain conifers (Podocarpaceae), but were unable to identify any clear pattern. Many environmental, historical and biological effects probably interact, with each of these effects varying greatly in ways that are poorly captured by available data sets. These effects must therefore be disentangled before a predictive model of African montane carbon distribution can be developed.
Tropical carbon sinks are saturating at different times on different continents
Nevertheless, Cuni-Sanchez and colleagues’ study underlines a crucial message: African montane forests are immensely valuable, and not only because they host the source of the River Nile, mountain gorillas and ecosystems such as mysterious lichen-covered forests. They also store vast amounts of carbon, and thereby have a key role in tackling climate change. Of course, this immense intrinsic value does not preclude intense human exploitation of these ecosystems, which can lead to rapid degradation and deforestation. For instance, on the basis of satellite monitoring, Cuni-Sanchez and colleagues report that Mozambique lost nearly one-third of its montane forests between 2000 and 2018.There is, however, the faint hope that putting a financial value on carbon, and the establishment of economic incentives to avoid deforestation in tropical countries, might help to check the flood of damage5. The aim is to reward African countries — for which montane forest sometimes constitutes the last remaining forests — for their conservation endeavours, and for renouncing efforts to access the timber and ore in these ecosystems, even when such resources are otherwise desperately lacking. By gathering the best-available data to provide precise, country-level estimates of average aboveground carbon content in African montane forests, Cuni-Sanchez and colleagues’ study will add weight to such efforts — not least because the new estimates are, on average, two-thirds higher than the values reported by the Intergovernmental Panel on Climate Change6.The next step should be to extend measurements in these forests, particularly by continuing to support national forest-inventory efforts. These inventories target all vegetation types, rather than just the most intact forests, and all carbon pools, using standardized protocols and systematic sampling methods. Remote sensors, both in the sky and in space, should also be used to fully map the detailed spatial variation of forest diversity, structure and dynamics. But there is no excuse for delaying policymaking — we already know enough to justify immediate decisive action to preserve yet another of Earth’s threatened treasures.

Nature 596, 488-490 (2021)
doi: https://doi.org/10.1038/d41586-021-02266-3

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The author declares no competing interests.

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In place of its normal load of cars and vans, the repurposed ferry boat sported a mobile science laboratory and a large fan on its deck as it left Townsville, Australia, in March. Researchers dropped anchor in a coral lagoon some 100 kilometres offshore and then fired up the cone-shaped turbine, which blew a mist of seawater off the back of the boat. What happened next came as a welcome surprise: after briefly drifting along the ocean surface, the plume ascended into the sky.Looking a bit like a jet engine, this mist machine is at the centre of an experiment that, if successful, could help to determine the future of the Great Barrier Reef. Three-hundred and twenty nozzles spewed a cloud of nano-sized droplets engineered to brighten clouds and block sunlight — providing a bit of cooling shade for the coral colonies below. Scientists used sensors aboard the ferry, drones and a second boat to monitor the plume as it migrated skyward.The experiment wasn’t big enough to significantly alter the clouds. But preliminary results from the field tests — which were shared exclusively with Nature — suggest that the technology might perform even better than computer models suggested it would, says Daniel Harrison, an oceanographer and engineer at Southern Cross University in Coffs Harbour, Australia, who is heading up the research. “We are now very confident that we can get the particles up into the clouds,” Harrison says. “But we still need to figure out how the clouds will respond.”Harrison’s project is the world’s first field trial of marine cloud brightening, one of several controversial geoengineering technologies that scientists have studied in the laboratory for decades. The research has been driven by fear that humans might one day be forced to deliberately manipulate the Earth’s climate and weather systems to blunt the most severe impacts of global warming.For many Australians, that day arrived in 2017, when a marine heat wave spurred massive coral bleaching and death across much of the 2,300-kilometre Great Barrier Reef. That crisis hit just a year after another bleaching event along the reef, which supports more than 600 species of coral and an estimated 64,000 jobs in industries such as tourism and fishing. Research suggests that the reef lost more than half of its coral between 1995 and 2017, as a result of warming waters, tropical storms and predatory starfish (A. Dietzel et al. Proc. R. Soc. B. 287, 20201432; 2020).
These corals could survive climate change — and help save the world’s reefs
The project has raised concerns among some scientists abroad, in part because the Australian group has published little about its work. Environmentalists outside Australia objected to the project last year after news of the first trial broke, and there could be similar criticism when details of the 2021 trial emerge.Harrison stresses that the cloud-brightening project is about local adaptation to climate change, not global geoengineering, because its application would be limited in both space and time. It’s also just one part of a larger Aus$300 million (US$220 million) Reef Restoration and Adaptation Program (RRAP) launched last year by Australia to investigate and develop techniques and technologies to save the country’s reefs. Many of the proposals, from cloud brightening to breeding heat-tolerant corals, would represent unprecedented human interventions in the natural reef system.Ecological modelling suggests that a large-scale intervention involving multiple strategies — including a fleet of mist machines — could prolong the life of the reef while governments work to eliminate greenhouse-gas emissions. The goal now is to work out what’s achievable in the real world, says Cedric Robillot, executive director of the RRAP.“You need to consider every angle, from the fundamental science to the very pointy end of engineering, if you want to succeed,” Robillot says. “It’s not enough to just prove you could do it. You need to explain how you would do it.”Into the cloudsHarrison conducted his first field test in March 2020: a three-day proof-of-concept expedition on a small car ferry with four scientists, one representative from a local Indigenous group, and two shipping containers for equipment and sleeping quarters. The team had a minimal Aus$400,000 budget and limited scientific instrumentation to monitor the mist, but it was enough to document that the plume flowing out of their mist machine rode a draught of warm air high into the sky.It was the first time they had witnessed this phenomenon. Their models had suggested that evaporation of the brine droplets would cool the plume, which would then float across the surface of the ocean, only slowly mixing upwards into the low-lying marine clouds. The models also indicated a risk that the tiny droplets might merge and drop out of the air. Instead, brine droplets floated along the surface of the ocean for half a kilometre without coalescing, gradually losing water and weight to evaporation along the way. And then they shot upwards.

A marine heat wave in 2017 caused coral bleaching along much of Australia’s Great Barrier Reef.Credit: Juergen Freund/Nature Picture Library

“We didn’t expect that at all,” Harrison says, “but it turned out we were doing this experiment in the middle of a rising air mass.”The scientists feared it was a fluke. Although years of research and development have gone into the nozzles, initially led by a separate American team, this was the first time anybody had ever deployed them in the field with fresh seawater. The team also didn’t know what to expect from clouds and aerosols in that region, because research on the reef has focused almost exclusively on what happens below the water, not the conditions above.For Harrison, the 2020 experiment was more than enough to justify moving forward with another, larger trial in March 2021. But it did raise eyebrows among some scientists and observers abroad, where geoengineering research has met strong opposition and struggled to attract funding.
IPCC climate report: Earth is warmer than it’s been in 125,000 years
Most of the concern has centred on a form of solar geoengineering that involves injecting reflective material into the stratosphere to block sunlight at a global scale. But cloud brightening has also been studied as a potential global intervention, and it has attracted criticism from some environmental groups who argue that it carries inevitable ecological risks and detracts from efforts to limit greenhouse gases.Some scientists, as well as environmental advocates who follow geoengineering research, told Nature that they were surprised to see the experiment move forward without more scrutiny — or without published research to justify such an investment.Critics also worry that Australia is setting the wrong kind of precedent by rebranding a solar-geoengineering experiment that could have regional impacts as a local adaptation project. “One could say that there should have been some level of consultation with the outside world,” says Janos Pasztor, who heads the Carnegie Climate Governance Initiative, an advocacy group in New York City that has been pushing for a global debate over geoengineering governance in the United Nations.Harrison says scientists in the programme have consulted with regulatory authorities, as well as with the general public and Indigenous groups that have historic claims on the reef. He also readily acknowledges trying to avoid getting embroiled in a debate about solar geoengineering, arguing that the project would be more akin to cloud-seeding operations that are designed to promote rain and that are not considered to be geoengineering. One of the next modelling efforts, however, will be to explore any potential regional and global implications, he says.

A plume of seawater droplets rises up into the sky during a field trial in March 2021.Credit: Brendan Kelaher/SCU

Others question the Australian government’s motivations in funding such work. Under the conservative prime minister Scott Morrison, the government has yet to strengthen its climate pledge under the 2015 Paris agreement, as many nations have done in the past year. Morrison has personally ruled out committing to net-zero emissions. Pushing for a technological fix to global warming without moving to aggressively curb greenhouse gases is “sheer lunacy”, says Peter Frumhoff, chief climate scientist for the Union of Concerned Scientists, an advocacy group in Cambridge, Massachusetts.Some researchers, however, are pleased to see marine cloud brightening move from theory to the field, including US scientists working on a similar project that has been struggling to get into the field for nearly a decade. “This is an early example of how climate disruption can drive interest in these things,” says Sarah Doherty, an atmospheric physicist who manages the Marine Cloud Brightening Project at the University of Washington in Seattle. Members of the team provided the initial nozzle design and have been tracking the Australian group’s progress.Coral crisisThe first time that scientists observed a major bleaching event along the Great Barrier Reef was in 1998, and the second event followed four years later. In both cases, corals expelled the algae that live within them and that provide colour and energy through photosynthesis. Most of the corals eventually recovered. But in 2016 and 2017, many corals bleached and then died across two-thirds of the reef.
First sun-dimming experiment will test a way to cool Earth
“It was absolutely horrifying,” says David Wachenfeld, chief scientist at the Great Barrier Reef Marine Park Authority, which manages the reef. The clear message from those events was that the traditional approach to managing corals and coral reefs would not be enough, he adds. “Our hand was forced.”In 2018, the Australian government allocated Aus$6 million to a consortium of universities and government research institutes for a feasibility study focused on potentially radical strategies that could be applied across the reef. Researchers reviewed some 160 ideas, including putting live corals on ice for long-term preservation and synthetically engineeering new varieties that can tolerate the warmer waters. Many approaches proved too costly and energy intensive, but 43 interventions were singled out for further study. Marine cloud brightening drew support in part because it theoretically provides direct relief precisely when and where corals need it most.Much of the emphasis of the programme is on helping corals to adapt and repopulate the reef, including efforts to improve coral aquaculture operations so that they can produce millions of corals per year rather than thousands. For Madeleine van Oppen, a coral geneticist at the Australian Institute of Marine Science near Townsville, the RRAP programme helps to integrate her team’s work on assisting coral evolution to make them more heat tolerant.Thanks to the RRAP, she says, data from those projects are now being fed directly into models that enable researchers to assess the potential benefits — as well as the risks — of releasing new strains of coral and microalga into the wild. The programme is also raising ecological questions, such as whether the introduction of new coral species can propagate disease, or whether a new variety of more heat-tolerant corals might displace corals struggling to survive.

Researchers are testing specialized nozzles that create jets of seawater mist.Credit: Alejandro Tagliafico/SCU

“It sort of speeds up the whole path from research to implementation in the field,” says van Oppen.In the long run, the models indicate that without interventions, the extent of coral on the reef could shrink by well over 60% by 2070 compared with 2020 levels (S. A. Condie et al. R. Soc. Open Sci. 8, 201296; 2021). But simulations suggest that Australia could cut those losses in half with a three-pronged approach focused on propagating heat-tolerant corals, controlling outbreaks of the predatory crown-of-thorns starfish and brightening clouds to take the edge off of heat waves. Crucially, the latest modelling also suggests that without the cooling provided by Harrison’s cloud brightening project, the other interventions might not amount to much.Testing the windWhen Harrison’s group returned to the field this year, they had more-powerful drones as well as other aerosol sensors on a second boat. As in the previous year’s experiment, each time they created a plume, it rose into the sky after the droplets lost around 90% of their water to evaporation. The likely explanation, Harrison says, is that the reef is creating its own weather as warm water along the shallow corals heats the air above.Many more droplets are making it into the clouds than the scientists had initially calculated, but Harrison says their mist machine might need to be scaled up by a factor of 10 — from 320 to around 3,000 nozzles — to produce enough particles to brighten nearby clouds by around 30%. His team’s modelling suggests that this could in turn reduce the incoming solar radiation on the reef locally by around 6.5%. Even then, the operation would require 800–1,000 stations to cover the length of the Great Barrier Reef.
Fevers are plaguing the oceans — and climate change is making them worse
But it’s unclear whether that spray of salty droplets will have the desired effect, says Lynn Russell, an atmospheric chemist at the Scripps Institution of Oceanography in La Jolla, California, who has studied cloud brightening. Russell has not seen the latest — and as-yet unpublished — results, but questions whether there are enough of the low layered clouds considered suitable for cloud brightening.Harrison acknowledges such concerns and says that his team sees more of these clouds on the southern part of the reef. His team’s modelling suggests the technology will also work on the clouds that are common across the rest of the reef in summer. Even then, he says, it remains unclear how much coverage a full-scale cloud-brightening operation could provide across the entirety of the reef. More measurements, and detailed modelling, are needed to provide answers.For now, Harrison has secured funding for another two years, and he needs to demonstrate progress. The RRAP is testing all 43 approaches and will redistribute resources to projects that show potential, Robillot says. But he stresses that no amount of science and engineering will preserve the reef in its current form. “Even if we do all of this, the system that you’ll end up with is not going to be the Great Barrier Reef that we know today,” Robillot says. “You might, however, retain a very functional ecosystem.”That’s enough to keep Harrison going, and his team is already preparing for a trip into the field in 2022. The scientists plan to run the mist machine at higher pressure, which should produce a sixfold increase in the number of particles, and they will use new instrumentation to determine how particles alter clouds. They are also investigating an entirely different nozzle technology that could reduce the number of nozzles needed by a factor of 1,000.Harrison is more confident today than he was even a year ago that cloud brightening might work over the reef, but he is also realistic about the future if governments fail to limit carbon emissions. “There are only so many clouds available, and there is only so much you can brighten them,” he says. “Eventually, climate change just overwhelms things.”

Nature 596, 476-478 (2021)
doi: https://doi.org/10.1038/d41586-021-02290-3

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Conceptualization of organismal to tumor biogeography through clone phylogeniesWe first map organismal biogeographic concepts and models to the process of migration and colonization of cancer cells during metastasis. Tumors are populations consisting of a diversity of cancer cells with different genetic profiles that may represent different lineages in the clone phylogeny. We use the example in Fig. 1, which contains a phylogeny of 17 clones found in one primary tumor (P) and four metastases (M1–M4). Events occurring along a branch in a phylogeny are anagenetic events, which include diversification, extinction, and expansion12,14. In organismal evolutionary biology, anagenetic events are not directly observed except through the fossil record. However, one can map the collection of genetic variants that likely arose on individual lineage in a phylogeny. In many cancers, sequencing of temporally sampled biopsies’ can directly reveal anagenetic events similar to the sequencing of ancient DNA in paleogenomics.The other types of evolutionary events in the phylogeny are cladogenetic, including genetic divergences and dispersals (Fig. 1). Genetic differences observed among species and populations are the key to detect cladogenetic events reconstructed in molecular phylogenies of living descendants. In cancer, temporal sampling of biopsies can reveal cladogenetic events that produced extinct descendants.In biogeography, genetic divergence results in the diversification of lineages within an area. Sometimes, the term duplication is used, but we avoid its further use because of the confusion it may cause in evolutionary genomics. Divergence events are also observed in a clone phylogeny, particularly when clone lineages diverge from each other within a tumor or across tumors. The exact opposite of genetic diversification can also be observed when lineages partially or fully disappear from the phylogeny. Extinction can occur due to random chance, selection, or environmental pressures. Even though extinction is rarely discussed in tumor clone phylogenetics, it happens frequently.Phylogenies also reveal movements of lineages between locations (geographic areas or body parts) when the locations of individual cells, species, or populations are known5,6,7,8,9,15. When lineages accumulate genetic differences along a branch in the phylogeny, and the evolved lineages migrate to a new area, we observe an expansion event. Expansions differ from dispersals in such that the growth of a population occurs in the same place. This movement of cells of a clone from one location to another, where they would potentially form a metastasis, results in the dispersal of  these cells of that clone to additional areas, which is modeled by a dispersal rate (d) in organismal biogeography. When a clone genetically diverges following its migration, then a distant dispersal event is said to have occurred. Similarly, when a clone diverges from the rest of the clones within a tumor and disperses to another tumor, we have observed an expansion event. Thus, clone phylogenies can give insights into the origin and trajectory of cancer cells between tumors.When a clone is no longer present at a location, it is extinct at that location. Extinctions are modeled by an extinction rate (e) in biogeographic models. As a result of extinction, the range of descendent clones on a phylogeny can be smaller than the ancestors. Biogeography models also have a parameter (J) to consider founder events that establish new populations from a few individuals. In phylogenies, founder events can be detected if only one or a few cells are found to have moved from one location to another to start diversifying in a new area. Both distant dispersal and founder events may result in forming a new colony of cells, i.e., a new metastasis in the case of cancer cell migrations. The primary distinction between dispersal and founder events is the relative number of migrating cells. Founder events are due to one or a few cells, whereas dispersal events involve a larger number of migrating cells. Founder events are expected to be more common in tumor evolution because metastases are thought to be formed by the spread of only one or a few cancer cells. These biogeographic events have been mathematically modeled and implemented in various approaches to infer species migration events12, which are directly applicable in the inference of cancer cell migrations between tumors.Model fitsWe began by analyzing the statistical fits of six biogeographic models (Table 1) to 80 computer-simulated tumor evolutionary datasets. Simulations enable us to assess the performance of computational approaches and reveal potential caveats associated with their use because the ground truth is known. These datasets were simulated using four main clone migration schemes defined by the different number of migrating clones (1–3), the small and large number of tumor areas (5–7 tumors, m5 datasets; 8–11 tumors, m8 datasets), and the different types of source areas of migration (primary or metastasis). The following seeding scenarios reflect this complexity of the clone migration schemes: monoclonal single-source seeding (mS), polyclonal single-source seeding (pS), polyclonal multisource seeding (pM), and polyclonal reseeding (pR) (see “Methods” section).Table 1 Phylogenetic and biogeographic events considered in seven biogeographic models used for analysis.Full size tableWe considered biogeographic models that weigh genetic divergence, dispersal/expansion, and extinction events differently (Table 1). We also explored the provision of including founder events in our models on the accuracy of detecting clone migrations. The parameterization of the aforementioned events results in models with two free parameters, i.e., dispersal rate (d) and extinction rate (e), and models with three free parameters by adding the founder-event speciation (J); see “Methods” section for more details.Overall, we tested six biogeographic models for their fit to the tumor data, three models with two free parameters and three others with three free parameters. BAYAREALIKE, DEC, and DIVALIKE models have two parameters each. They are nested within their respective models that add the founder effect, resulting in a model with three free parameters (hereinafter +J models). We used the BioGeoBEARS software for all model fit analyses. In data analysis, we first inferred phylogeny of cancer cell populations (clone phylogeny) using an existing method16, followed by the use of BioGeoBEARS to infer the clone migration history in which the clone phylogeny is used along with the location of tumor sites in which each clone is observed (Fig. 2). BioGeoBEARS estimates the probabilities of annotating internal nodes with tumor locations. These annotations are then used to derive cancer cell migration paths when two adjacent nodes are annotated with different tumor locations. In these analyses, we assumed the correct clone phylogeny because our focus was not assessing the impact of errors in a phylogeny on the accuracy of clone migration inferences. We also compared the accuracy of migration histories reconstructed using biogeographic models in BioGeoBEARS with those obtained from the approaches that do not model biogeographic processes (BBM9, MACHINA5, and PathFinder7).Figure 2Data analysis pipeline using BioGeoBEARS in R14 to infer clonal migration histories.Full size imageWe first conducted Likelihood Ratio Tests (LRTs) to examine the improvement offered by considering founder events in modeling tumor migrations. In this case, the fit of the BAYAREALIKE, DEC, and DIVALIKE models was compared to their +J counterparts, respectively. The null hypothesis was rejected for more than 50% of the datasets (BAYAREALIKE: 71.25%, DEC: 60%, and DIVALIKE: 53.75%; P  More

The Fur-regulated T6SS1 plays an important role in iron acquisition in C. necator
To explore the function of T6SS1 (Reut_A1713 to Reut_A1733) in C. necator (Fig. S1A), we analyzed the T6SS1 promoter and identified a Fur binding site (AGAAATA) upstream of gene reut_A1733. This Fur binding site was highly similar to the Fur-box reported in E. coli [38], with a probability score of 2.25 (out of a maximum score = 2.45) (Fig. S1B), which was calculated by applying the position weight matrix to a sequence [39]. Incubation of the T6SS1 promoter probe with purified Fur protein led to decreased mobility of the probe in the electrophoretic mobility shift assay, suggesting a direct interaction between Fur and the T6SS1 promoter (Fig. 1A). To further determine the function of Fur on the expression of T6SS1, a single-copy PT6SS1::lacZ fusion reporter was introduced into the chromosomes of C. necator wild-type (WT), Δfur deletion mutant, and the Δfur(fur) complementary strain. Compared to WT, the PT6SS1::lacZ promoter activity was significantly increased in the Δfur mutant (about 2.2-fold), and this increase could be restored by introducing the complementary plasmid pBBR1MCS-5-fur (Fig. 1B). Similar results were obtained by analyzing the expression of T6SS1 core component genes (hcp1, clpV1, vgrG1, and tssM1) with qRT-PCR (Fig. S1C). These results demonstrate that the expression of T6SS1 in C. necator is directly repressed by Fur, the master regulator of genes involved in iron homeostasis in many prokaryotes [40, 41].Fig. 1: Regulation of T6SS1 expression by Fur.A The interactions between His6-Fur and the T6SS1 promoter examined by EMSA. Increasing amounts of Fur (0, 0.03, 0.06, 0.13, 0.25, and 1.0 μM) and 10 nM DNA fragments were used in the assay. A 500 bp unrelated DNA fragment (Control A) and 1 µM BSA (Control B) were included in the assay as negative controls. B Fur represses the expression of T6SS1. β-galactosidase activities of T6SS1 promoter from chromosomal lacZ fusions in relevant C. necator strains were measured. C Iron uptake requires T6SS1. Stationary-phase C. necator strains were washed twice with M9 medium. Iron associated with indicated bacterial cells were measured with ICP-MS. The vector corresponds to the plasmid pBBR1MCS-5 (B) and pBBR1MCS-2 (C), respectively. Data are represented as mean values ± SD of three biological replicates, each with three technical replicates. **p  More

AffiliationsAnimal Production Systems group, Wageningen University & Research, Wageningen, The NetherlandsAbigail Muscat, Evelien M. de Olde, Raimon Ripoll-Bosch & Imke J. M. de BoerFarming Systems Ecology group, Wageningen University & Research, Wageningen, The NetherlandsHannah H. E. Van ZantenPublic Administration and Policy group, Wageningen University & Research, Wageningen, The NetherlandsTamara A. P. Metze & Catrien J. A. M. TermeerPlant Production Systems group, Wageningen University & Research, Wageningen, The NetherlandsMartin K. van IttersumAuthorsAbigail MuscatEvelien M. de OldeRaimon Ripoll-BoschHannah H. E. Van ZantenTamara A. P. MetzeCatrien J. A. M. TermeerMartin K. van IttersumImke J. M. de BoerCorresponding authorCorrespondence to
Imke J. M. de Boer. More