Ecology

Total P and available P
Fertilizer application significantly (P  0.05). The highest increase in available P concentration in NPK + S treatment observed in the 60–100 cm soil depth, with the increase of 111% and 115% in 60–80 cm and 80–100 cm soil depths, respectively, over CK treatment.
Figure 2

Effect of long-term application of chemical fertilizer, organic manure, and straw on total phosphorus (P) and available P concentrations. * indicates significant difference at P  3.6%) was associated with OM treatment, especially at the 0–20 and 20–40 cm soil depths (Fig. 3). The PAC values under NPK, NPK + S and OM treatments increased by 7.6%, 4.5% and 11.5% in the 0–20 cm soil depth and 4.2%, 1.3%, and 5.8% in 20–40 cm soil depth, respectively as compared to the CK treatment. However, PAC value for soil depth below 40 cm showed the trend, NPK  More

NEWS AND VIEWS
09 September 2020

How can the decline in global biodiversity be reversed, given the need to supply food? Computer modelling provides a way to assess the effectiveness of combining various conservation and food-system interventions to tackle this issue.

Brett A. Bryan &

Brett A. Bryan is at the Centre for Integrative Ecology, Deakin University, Melbourne, Victoria 3125, Australia.
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Carla L. Archibald

Carla L. Archibald is at the Centre for Integrative Ecology, Deakin University, Melbourne, Victoria 3125, Australia.

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Nature is in trouble, and its plight will probably become even more precarious unless we do something about it1. Writing in Nature, Leclère et al.2 quantify what might be needed to reverse this deeply worrying path while also feeding people’s increasingly voracious appetites. The authors’ answer is to team ambitious conservation measures with food-system transformation in the hope of reversing the trend of global terrestrial biodiversity loss.

By nature, we mean the diversity of life that has evolved over billions of years to exist in dynamic balance with Earth’s biophysical environment and the ecosystems present. Nature contributes to human well-being in many ways, and the services it provides, such as carbon sequestration by plants or pollination by insects, could impose a vast cost if lost3. Although the slow and long-term decline of Earth’s biodiversity4 is often overshadowed by climate change, and more recently by the COVID-19 pandemic, the loss of biodiversity is no less of a risk than those posed by the other challenges. Many would argue that the effect of biodiversity losses could surpass the combined impacts of climate change and COVID-19.
More and more, the realization is growing that, as a planet, we are what we eat. Human demand for food is accelerating with the ever-increasing global population (projected to approach 10 billion by 2050), and each successive generation is wealthier and consumes more resource-intensive diets than did the previous one5. Trying to balance this rapidly rising demand against the limited amount of land available for crops and pasture sets agriculture and nature (Fig. 1) on a collision course6. As Leclère and colleagues show, a bold and integrated strategy is required immediately to turn this around.

Figure 1 | A bean field bordering a rainforest reserve near Sorriso, Brazil.Credit: Florian Plaucheur/AFP/Getty

Taking a long view out to the year 2100, Leclère et al. present a global modelling study assessing the ability of ambitious conservation and food-system intervention scenarios to reverse the decline, or, as they call it, “bending the curve”, of biodiversity losses resulting from changes in agricultural land use and management. Projections of future land use and biodiversity are uncertain, and when these models are combined, this uncertainty is compounded. One of the great innovations of Leclère and colleagues’ work is in embracing this uncertainty by combining an ensemble of four global land-use models and eight global biodiversity models and measuring the performance of future land-use scenarios in terms of higher-level model-independent metrics such as the amount of biodiversity loss avoided.
Importantly, the study also included a baseline (termed BASE) scenario — the world expected without interventions — and Leclère et al. used this to gauge the effectiveness of the intervention scenarios. Although it is not a focus of the paper, it’s worth pausing to ponder the sobering picture painted by this business-as-usual future largely bereft of birdsong and insect chirp.
Choosing to act now can make a difference to nature’s plight. Most (61%) of the model combinations run by the authors indicated that implementing ambitious conservation actions led to a positive uptick in the biodiversity curve by 2050. Such conservation actions included: extending the global conservation network by establishing protected nature reserves; restoring degraded land; and basing future land-use decisions on comprehensive landscape-level conservation planning. This comprehensive conservation strategy avoids more than half (an average of 58%) of the biodiversity losses expected if nothing is done, but also leads to a hike in food prices.

When conservation actions were teamed with a range of equally ambitious food-system interventions, the prognosis for global biodiversity in the model was improved further. Including both supply- and demand-side measures, these approaches included boosting agricultural yields, having an increasingly globalized food trade, reducing food waste by half, and the global adoption of healthy diets by halving meat consumption. These combined measures of conservation and food-systems actions avoided more than two-thirds of future biodiversity losses, with the integrated action portfolio (combining all actions) avoiding an average of 90% of future biodiversity losses. Almost all models predicted a biodiversity about-face by mid-century. These food-system measures also avoided adverse outcomes for food affordability.
Leclère and colleagues’ work complements the current global climate-change scenario framework (tools for future planning by governments and others, including scenarios called shared socio-economic pathways, which integrate future socio-economic projections with greenhouse-gas emissions), and represents the most comprehensive incorporation of biodiversity into this scenario framing7 so far. However, a major limitation of the present study is that it does not consider the potential impact of climate change on biodiversity. This raises an internal inconsistency because, on the one hand, the baseline scenario considers land-use, social and economic changes under approximately 4 °C of global heating by 21008, yet, on the other hand, it does not consider the profound effect of warming on plant and animal populations and the ecosystems they comprise9. Also absent from the models were other threats to biodiversity, including harvesting, hunting and invasive species10. Although Leclère and colleagues recognized these limitations and assigned them a high priority for future research, unfortunately for us all, omitting these key threats probably means that the authors’ estimates of biodiversity’s plight and the effectiveness of integrated global conservation and food-system action are overly optimistic. To truly bend the curve, Leclère and colleagues’ integrated portfolio will need to be substantially expanded to address the full range of threats to biodiversity.
Although the models say that a better future is possible, is the combination of the multiple ambitious conservation and food-system interventions considered by Leclère et al. a realistic possibility? Achieving each one of the conservation and food-system actions would require a monumental coordinated effort from all nations. And even if the global community were to get its act together in prioritizing conservation and food-system transformation, would such efforts come in time and be enough to save our planet’s natural legacy? We certainly hope so.

doi: 10.1038/d41586-020-02502-2

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Properties of permafrost soils
All sites contained syngenetic permafrost in which the active layer and the uppermost permafrost have experienced numerous freeze-thaw cycles since formation during the Holocene22. Permafrost organic matter radiocarbon ages ranged from 7850 ± 30 to 830 ± 20 y B.P. (Supplementary Data), with the western sites containing the oldest SOM and the northern Hudson Bay peatlands containing the youngest SOM.
For organic layers, permafrost soil C:N atomic ratios (14.50 [12.61–19.67], median [25th–75th]) were lower and H:C atomic ratios (0.13 [0.13–0.14]) were greater relative to the active layer, 23.89 [19.33–29.50] and 0.14 [0.12–0.15], respectively (Supplementary Fig. 1). Similarly for mineral layers, permafrost C:N ratios were lower (12.0 [3.23–18.09]) and H:C ratios higher (0.24 [0.15–0.86]) compared to the active layer, 16.21 [13.67–18.87] and 0.17 [0.15–0.21], respectively. For both thermal layers, in organic layers C:N ratios were higher and H:C ratios were lower than in mineral layers.
These stoichiometric properties are typical of boreal and tundra soils (Supplementary Fig. 1)23. The higher C:N and very low H:C ratios of the organic layers relative to mineral layers suggest higher contents of condensed aromatic structures originating from peat24. Permafrost layers displayed lower C:N properties suggesting different SOM composition (e.g., lignin, tannins, lipids, sugars or amino acids) and an enrichment in microbial biomass relative to the active layer24. The absence of a downward trend of C:N and H:C within the permafrost (Supplementary Fig. 1), except at Daring Lake, indicates that soil development and microbial processing were effectively halted soon after permafrost aggradation23.
Active layer and permafrost yields of DOC and nitrogen
DOC content correlated with soil C content in both active layer (r2 [log–log] = 0.748, P  More

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Genome structure of DhNV
The circular genome of DhNV is 119,754 bp and contains 106 hypothetical ORFs, with 56 on the positive strand and 50 on the negative strand (Fig. 1). Fifty-nine of the ORFs met our comparative e-value threshold of  More

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Study site
The study was conducted in the Tone river basin, central Japan (Fig. 1). The Tone river is Japan’s second-longest river, running through the entire Kanto plain in central Japan. The Tone river basin is covered mainly by rice paddies and also contains arable fields other than rice, seminatural grasslands, coppice forests, farm villages, and urban areas29. The Tone river basin is located in the Kanto plain which is the largest plain field in Japan (approximately 170,000 km2), including large floodplains. Thus, this area have a variety of both terrain conditions and agricultural modernization works.
Figure 1

Location of the Tone river basin and monitoring sites.

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Plants community data
The Institute for Agro-Environmental Sciences, NARO, Japan conducted the program for monitoring biodiversity, including birds29 and plants34, in each of the thirty-two 1-km2 grids in the Tone river basin in 2002. In this program, the Tone river basin was initially divided into one hundred 1-km square grids (hereafter, 1-km grid), and each square was classified into one of four major land use types in the region: (1) midstream paddy; (2) downstream lowland paddy; (3) plateau and valley-bottom paddy; and (4) urban fringe29. Then, eight grids were selected randomly as study sites from each land use type, making a total of 32 grids (Fig. 1). The grids were more than 5 km apart (Fig. 1), so they were spatially independent of each other. In this study we used the plant monitoring records from the program. In the plant monitoring program there were three terms—2002, 2007, and 2012—of vegetation survey based on the Braun–Blanquet approach in each 1 km grid 35. In each survey, approximately 20 quadrats measuring 1 m2 were placed randomly in each 1-km grid in each survey term and the coverage ratios of all plant species in four hierarchies—(1) tall tree, (2) semi-tall tree, (3) shrub, and (4) grasses—were recorded. In this study, we used only the grasses class without abundance and the presence or absence of species records in the grasses class. We pooled all the species records within each 1-km grid for analysis. All plant monitoring data are available as Open Data (CC BY 4.0) at github space own by Dr. N. Iwasaki who was the member of this monitoring program (https://github.com/wata909/RuLIS_monitoring, accessed at 25, May 2020).
Dividing wetland plants and non-wetland plants
To test our hypothesis, we needed to divide the plants that typically grow in wetlands (hereafter, wetland plants) and those that typically grown in non-wetlands (hereafter, non-wetland plants) to evaluate the habitat quality of paddy fields as wetland. To this end, we used a published checklist of wetland plants in Japan (Shutoh et al. 2019; https://wetlands.info/tools/plantsdb/wetlandplants-checklist/, accessed at 25, May 2020). This checklist defined 8,358 Japanese vascular plants as wetland and aquatic plants according to their habitat requirements and the “wetland” definition of the Ramsar Convention (Ramsar Convention Secretariat 2016, https://www.ramsar.org/sites/default/files/documents/library/manual6-2013-e.pdf, accessed at 25, May 2020). We used this checklist to identify the wetland plant species in the monitoring records.
Land use, terrain condition, and human activity
A digitized land use map for paddy fields in 2009 that relatively matched the plant monitoring terms (2002, 2007, and 2012) was prepared from the National Land Numerical Information (National Land Information Division, MLIT of Japan: https://nlftp.mlit.go.jp/ksj-e/index.html, accessed at 25, May 2020). These map data were developed using both topographic maps and satellite imaging data, with the land use labeled on the basis of nationwide land use classifications, including paddy fields, at approximately 100-m grid resolution (National Land Information Division, MLIT of Japan: https://nlftp.mlit.go.jp/ksj-e/index.html, accessed at 25, May 2020).
A FAV, which was ascertained by accumulating the weights of all cells that flowed into each downslope cell, was used to define the concave areas (ESRI, https://pro.arcgis.com/en/pro-app/tool-reference/spatial-analyst/how-flow-accumulation-works.htm, accessed at 25, May 2020); lower elevations and valley areas had a higher FAV because they could potentially store more water, whereas higher ridge areas had low FAVs (Fig. 2). We used FAV to define the wetland potential, as this value could reflect the water accumulation from upper areas to lower areas, which strongly relates to the natural process of wetland formation36. We considered that terrain variable could reflect the geographical conditions of paddy field namely potentially wetland habitat for their intact ecosystem. We considered high FAV areas to have high potential of wetland habitat for their intact ecosystem. We calculated FAV value on a whole for mainland Japan; therefore, that range could cover the entire basin which overlapped with our target areas. The FAV was calculated using ArcGIS 10.5 with Spatial analyst (ESRI, Redlands, CA, USA) using a 50-m digital elevation model from the Japanese Map Centre (https://www.jmc.or.jp/, accessed at 25, May 2020). The FAV and paddy field maps were overlaid, and the total FAVs for paddy fields in each 1-km grid were calculated to determine the potentiality of the paddy fields in the 1-km grid being wetland. If a paddy field had an extremely high FAV within the basin which included the paddy field, that paddy field could have been a wetland because that area could store a large amount of water naturally.
Figure 2

Conceptual image of the flow accumulation value to indicate the potential of wetland.

Full size image

The proportional area of field consolidation as current human activity was calculated for each grid square using digital polygon data on the shape of farmland, as derived from aerial imagery collected in 2001 by the Ministry of Agriculture, Forestry, and Fisheries (MAFF), Japan. We obtained data on land leveling in agricultural areas from MAFF (https://www.maff.go.jp/j/tokei/porigon/, accessed at 25, May 2020) and used these data as an index of consolidated farmland because land leveling is one of the important components of agricultural consolidation in Japan4,23. Generally, agricultural consolidation in Japan involves land leveling, which integrates small, patchy farmland areas. Each polygon was assigned a status of “leveled” or “not leveled” according to its current status. Using ArcGIS, we calculated the ratio of consolidation for paddy fields in each 1-km grid that had survey sites.
Statistical analysis
We performed the two types of analysis used in this study with the statistical package R version 3.5.2 (R development core Team, https://www.r-project.org/, accessed at 17, Feb. 2020). First, we tested the species number in each 1-km grid using GLM with Poisson distributions (log link) and a Wald test37. The response variables were total species number, number of wetland plants, and number of non-wetland plants in each 1-km grid in each survey term. Explanatory variables were the log-transformed FAV values for the paddy fields and consolidation ratio of the paddy field within the 1-km grid. The aim of this analysis was to assess the effects on species diversity of both the original environmental condition of and current human activities in the paddy fields. Prior to the GLM analysis, all explanatory variables were tested for multicollinearity by calculating the variance inflation factors (VIFs)38; no significant multicollinearity was found (VIF  More

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