Philippa Kaur

Spatial patterns of stability proxies and background variables
Figure 2 a, b show the spatial distribution of our two proxy variables, the average rank of Rs per position (rankRs) and of the range of the ranks per position (rangeRs) in kriged maps. The middle to southern areas were found to have the largest, whilst the north-eastern areas the smallest rankRs values, whereas a slightly different pattern was characteristic for rangeRs with some additional north-western large values. Similarly, larger average soil organic carbon content (meanSOC) and average soil water content (meanSWC) (Fig. 2 c, d) were detected at the western-middle-southern regions and smaller at the north-eastern part of the study site.
Figure 2

Kriged patterns of stability proxies, rankRs (a) and rangeRs (b), as well as of background factors, meanSOC (%, c) and meanSWC (%, d).

Full size image

Correlations between stability proxies and background variables along DEMs: entire dataset
We investigated the potential direct effects of the different terrain attributes (local mean elevation (mALT), standard deviation of elevation (SD), topographic position index (TPI), slope (Sl), Easterness and Northness (East, North)) on the spatial distributions of our proxy variables by using the terrain attributes originating from differently smoothed DEM rasters. DEM1 was the original, 0.2 m resolution model, while DEMs 2–6 were progressively smoothed by a factor of two resulting in different resolution DEM rasters (DEM2: 0.4 m, DEM3: 0.8 m, DEM4: 1.6 m, DEM5: 3.2 m, DEM6: 6.4 m, respectively), and finally DEM7 met the resolution of the field measuring campaigns (10 m). The terrain attributes were filtered out from the rasters for the 78 measuring positions of the sampling grid.
On the basis of the correlation analysis we found an important difference in terrain attribute features between DEM 5 and 6, especially in SD, Sl, North and East. All subsequent results are then based on DEMs 1–5, which were found to be more similar to each other and to the original DEM1. The maps of terrain attributes with the box blur kernel from DEM1-5 can be found in the Supplementary Information (SI) together with the descriptions and calculations. As we couldn’t find any of the blur kernels superior to the other when considering correlations, the results hereafter are only presented for the box blur kernel calculations for simplicity.
When we considered the entire dataset (named hereafter: “A” dataset), we could only find significant correlation between rangeRs and TPI at less smoothed DEMs but the correlation was very weak (black symbols and line in Fig. 3).
Figure 3

Direct correlation between TPI and stability proxy, rangeRs at less smoothed DEMs, DEM1-2 for datasets A (black symbols and line) and S (blue symbols and line, see the information later on). The correlations were significant at p = 0.0076 and p  = 0.0172 levels, although they were weak, r2 = 0.09, r2 = 0.42 for A and S (see the information later on), respectively.

Full size image

Any other correlation between the proxies and the terrain attributes could only be deduced indirectly from the positive correlations between rankRs and meanSOC, meanSWC (cf. Table 1b). These correlations were scale-independent, i.e., we detected them at every DEMs. In general, the larger the soil carbon content and soil moisture at a position (cf. Figure 2c,d, showing quite similar patterns to the proxy patterns in the figure upper row), the larger the Rs activity detected and the opposite was true for lower carbon content and soil moisture positions.
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According to an initial keyword search, we selected the 17 most popular microbial ecology-related journals, as these were more likely to have sequence-specific data deposition instructions or requirements. We surveyed all the articles published in these journals between January 2015 and March 2019 (n = 26,927 articles, Supplementary Table S1), as concerns over data deposition practices began to grow in 201514 and were soon followed by stricter standards for data availability12. A custom-built pattern-based text extraction algorithm followed by manual curation, we selected those studies which performed 16S rRNA gene amplicon sequencing and listed INSDC-compliant accession numbers (n = 2015, Supplementary Table S1; 145,203 samples).
To confirm that our parsing algorithm did not miss accession numbers in articles containing 16S rRNA gene amplicon sequencing, we randomly selected 150 articles which mentioned 16S rRNA, but for which no accession numbers were detected, for manual inspection. Of these, one contained a misspelled accession number, two had archived their sequences in unconventional repositories (Google Drive and GEO, a gene expression database, Supplementary Data 2), and 19 were identified as having performed 16S rRNA gene amplicon sequencing, but had not included any reference to the data. We found no cases in which accession numbers or sequence data were stored in supplementary materials. From this group, we estimate that 18% of the studies in our database (n = 469) performed 16S rRNA gene amplicon sequencing but did not provide access to the data (Fig. 1a). Four studies mentioned deposition data in dbGaP18, and we could verify the existence of three of these studies. We found that an additional 6.5% of the studies had deposited their data in the Qiita19, MG-RAST20, and figshare databases (n = 14, n = 134, and n = 24 studies, respectively). Of the estimated 2,656 studies employing 16S rRNA gene amplicon sequencing, 75.9% deposited their data to an INSDC database in the period studied (Fig. 1a).
Fig. 1: Popular locations for data storage.

Data for all studies which contained 16S rRNA amplicon sequencing (a), and the V3–V4 subset (b); n = 2656 and n = 635 studies, respectively. For the entirety of the study, studies which contained amplicon sequences but did not deposit them were inferred by manually checking 150 randomly-selected articles which did not contain INSDC accession numbers or refer to alternative databases, indicated in lighter yellow. For the V3–V4 subset, studies which contained the keywords “16S rRNA”, “515”, and “806” were selected. Studies for which INSDC-compliant accession numbers were reported but which did not exist on any INSDC database are shown in lighter blue.

Full size image

To obtain more precise estimates of the percentage of articles which deposited their data in each database, we focused on the subset of 635 studies which sequenced the V3–V4 region of the 16S rRNA gene between base pairs 515 and 806 (heretofore V3–V4 subset), a target region which has gained popularity since its development and use by the Earth Microbiome Project21,22. Of these, 74.5% (n = 474) studies listed INSDC-compliant accession numbers within the article, but of these, accession numbers from 5% of the studies (n = 33) were not findable on any INSDC database. Additionally, 19% (n = 121) did not provide an identifiable link to the data, and 6.8% of the studies deposited their data in the Qiita, MG-RAST, and figshare databases (n = 9, n = 24, n = 7, respectively, Fig. 1b). Two studies provided SRA submission IDs rather than accession numbers, and were also inaccessible.
The increasing popularity of microbial community sequencing was evident in our data. Over the period studied, the number of studies in the V3–V4 subset rose from 56 in 2015 to 214 in 2018 (Supplementary Fig. 1a). The proportion of publications which claimed to deposit data to INSDC databases increased slightly over time, from 33/56 in 2015 to 172/214 in 2018 (χ2 = 6.6, p = 0.01, Supplementary Fig. 1b), suggesting an increasing tendency towards deposition in INSDC databases. Deposition to alternative databases decreased (χ2 = 14.04, p  More

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For predators, climate change-induced shifts in prey numbers, behaviours and spatial or temporal locations can be a major threat to food security. For predators that hoard prey to ensure survival through harsh winters, climate variation can have a doubled effect — influencing both food capture and store stability. Although northern latitude autumn and winter temperatures have increased dramatically in recent years, the effects of climate on foraging and storing throughout winter remain understudied.

Credit: Szymon Bartosz / Alamy Stock Photo

Giulia Masoero at the University of Turku, Finland, and colleagues analysed the impact of climate on Eurasian pygmy owl (Glaucidium passerinum) food-hoarding behaviour across 16 years. They found increased freeze–thaw frequency, lower winter precipitation and deeper snow cover were linked to greater hoard consumption. Higher autumn precipitation and an early hoarding start led to food rot, which reduced female owl recapture (indicating death or emigration).

Although owls delayed hoarding in autumns with fewer freeze–thaw events, suggesting some potential for climate change adaptation, the study indicates that altered climates can decrease owl overwinter survival, which may in turn have vast impacts on the boreal food web.

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Tegan Armarego-Marriott

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Armarego-Marriott, T. Owls’ hoards rot. Nat. Clim. Chang. (2020). https://doi.org/10.1038/s41558-020-0903-0
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