Philippa Kaur

Study site
The study sites were located approximately 20–75 km from the Fukushima Daiichi Nuclear Power Plant in Fukushima Prefecture, Japan (Fig. 1). According to an aircraft radioactivity survey reported by the Ministry of Education, Culture, Sports, Sciences, and Technology of Japan19, the air dose rate in this region was 0.3–3.2 μSv/h, and the deposition of cesium-134 and cesium-137 ranged from less than 64,000 to 940,000 Bq/m2 (Table 1) in June 2011. The study catchment area is mostly forested and dominated with deciduous trees. Other areas in the region are also forested as well, with Japanese cedar and cypress plantations used for timber production. A field survey was conducted at one headwater tributary (A) of the Nagase River and three headwater tributaries (B, C, and D) of the Kido River. The substrate of these sites was consisted with sand, cobble and rocks. Geological feature of the soil on all the sites was the same, biotite granite. Streams at sites B, C and D were covered with riparian forests and it was difficult for sunlight to penetrate directly. Stream width of site A was wider than sites B, C and D, so sunlight could penetrate through the forest cover and contact the stream surface only along the middle of the stream.
Figure 1

Study site in Fukushima Prefecture, Japan. Square: sampling sites, circle: FDNPP (Fukushima Daiichi Nuclear Power Plant). This map was generated by using software program Microsoft Paint Windows 10.

Full size image

Table 1 Air dose rate and the deposition of Cs according to an aircraft radioactivity survey by MEXT (2011), averaged value of dose rate 1-m above the ground on the sampling date from 2013 to 2019 (n = 23) and five environmental factors on four sites on the sampling date from 2013 to 2019 (n = 23).
Full size table

Sampling
The air dose rate at 1- m above the ground was measured with a γ survey meter at the sampling site (TCS-172 NaI scintillation counter; ALOKA). The electrical conductivity (EC) of the streams was measured using a portable compact twin conductivity meter (B-173; Horiba); pH was measured using a portable compact twin pH meter (B-212; Horiba), and the dissolved oxygen (DO) was measured using a portable DO meter (DO-5509; Lutron). Stream velocity was measured using a portable meter (V-303, VC-301, KENEK). All parameters were measured at all sites on all sampling dates.
Sand substrate, litter and algae were sampled from stream riffles at a depth of 10-15 cm from July 2013 to April 2019, as was reported in previous studies13. The sand substrate was sampled in each riffle to a depth of 5- cm. When sand was not immediately visible in the stream substrate, stones were removed and the sand underneath the stones was sampled. Litter shed in the water was collected after gentle hand-rinsing. Leaf litter forms the base of stream food webs. Periphytic algae were collected by brushing the pebbles or rocks with a toothbrush. These algae are also primary producers at the base of stream food webs. Prior to brushing, we gently hand-rinsed the stone surface to remove other organic matter and aquatic invertebrates in the periphyton.
Aquatic invertebrates from thirteen groups (Perlidae Gen. spp., Nemouridae Gen. spp., Ephemera japonica, Ephemerellidae Gen. spp., Heptageniidae Gen. spp., Hydropsychidae Gen. spp., Stenopsychi spp., Rhyacophilidae Gen. spp., Epiophlebia superstes, Lanthus fujiacus, Tipulidae Gen. spp., and Corydalidae Gen. spp., Geothelphusa dehaani,) were qualitatively sampled from riffles at a depth of 10-15 cm at the four sites from July 2013 to April 2019. At each site, a D-frame net with a 1-mm mesh was placed downstream of the sampling area on the substrate in water. We then disturbed the substrate upstream of the net, allowing insects to drift into the D-frame net. The sampled aquatic invertebrates were identified to family level in the field and then frozen.
Three bricks (210 × 100 × 60 mm) were placed separately within the stream riffle at a depth of 10–20 cm on August 25, 2014 at each of the four sites. Then, periphytic algae growing on the bricks were collected by brushing the substrate with a toothbrush. Before brushing, we gently hand-rinsed the brick surface in running water to remove other organic matter from the periphytic algae. The sampling was carried out eight times: in October and December 2014; March, May, June, July and November 2015; and April 2016. Stream velocity of right side, upper reaches side and left side of each brick were measured and averaged. This averaged value was used as the stream velocity of each periphytic algae sample.
Radiocesium analysis
Radiocesium was analysed according to the methods in previous studies10,20. Samples of sand substrate and litter were dried at 75 °C in an oven. Thereafter, samples of sand were placed in a sieve (mesh size 2 mm; Iida, Japan), and the sand that passed through the sieve was used, meaning that the sand substrate in this study included silt granules. Samples of algae were concentrated via evaporation and dried in an oven at 75 °C. Samples of aquatic invertebrates were also dried in an oven at 75 °C. All samples were homogenized and packed into 100-ml polystyrene containers (U-8). Gamma-ray spectrometric measurements were performed on each sample. The radioactive concentrations of cesium-134 (604 keV) and cesium-137 (662 keV) were measured using an HPGe coaxial detector system (GEM40P4-76, Seiko EG and G, Tokyo, Japan) at the Forestry and Forest Products Research Institute (FFPRI) with a time of 36,000 s or longer. Data with a standard error of  More

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To compare the establishment of human fecal bacterial communities in HMA mice and piglets, we inoculated GF mice and piglets maintained in gnotobiotic isolators with fecal matter from four separate human donors. The donors selected had diverse microbial communities (Fig. 1) and represented different stages of human development (see “Methods” for donor information). All animals in a given isolator (for both mice and piglets) were inoculated with the inocula obtained from a single donor. Both recipient species of animals were inoculated twice during the study—the initial round of inoculations were performed after weaning and the second round of inoculations occurred two weeks after the first round of inoculations. All inocula were prepared at the same time under the same conditions and both mice and piglets were fed the exact same sterile solid diet.
Fig. 1: Box-whisker plots comparing the alpha diversity of the inoculum aliquots among the different donors using the Shannon index.

Statistical comparisons were performed using the Wilcoxon rank-sum test. Boxes with different letters indicate statistically significant differences (p  More

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Affiliations

Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
Devi Veytia, Stuart Corney & Sophie Bestley

Australian Antarctic Division, Department of Agriculture, Water and the Environment, Kingston, Tasmania, Australia
Klaus M. Meiners & So Kawaguchi

Antarctic Climate and Ecosystems Cooperative Research Centre, University of Tasmania, Hobart, Tasmania, Australia
Klaus M. Meiners, So Kawaguchi & Sophie Bestley

British Antarctic Survey, Cambridge, UK
Eugene J. Murphy

Authors
Devi Veytia

Stuart Corney

Klaus M. Meiners

So Kawaguchi

Eugene J. Murphy

Sophie Bestley

Corresponding author
Correspondence to Devi Veytia. More

Collecting plant specimens
In the present study, 10 accessions assigned to 4 genera Atalantia, Luvunga, Paramignya, and Severinia were collected from different sites in Khanh Hoa and Lam Dong provinces of Vietnam (Fig. 1). Of these, six accessions of P. trimera (Oliv.) Burkill were collected at different sites in Khanh Hoa provinces including Ninh Van (PT1.NV, PT2.NV), Ninh Hoa (PT1.NH, PT2.NH), Dien Khanh (PT1.DK, PT2.DK); 1 accession of A. buxifolia (Poir.) Oliv. ex Benth collected in Van Ninh (PA.VN); 1 accession of S. monophylla (Lour.) Tanaka collected in Don Duong, Lam Dong province (PC.DD); two accessions of L. scandens (Roxb.), Wight, collected in Di Linh (PR.DL) and Cat Tien (PR.CT) in Lam Dong province (Fig. 1). The list of the collected accessions and information was summarized in Table 1.
Figure 1

Map of the sampling sites. Accessions of species P. trimera (Oliv.) Burkill, A. buxifolia (Poir.) Oliv. ex Benth, S. monophylla (Lour.) Tanaka, and L. scandens (Roxb.), Wight were collected at sites displayed as circles in the map. The map was created by using ArcGIS 10.3 using the color rendering and grouping tools built-in and Paintbrush version 2.5 (20190914) on mac OS Catalina.

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Table 1 List of the collected accessions and information.
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Taxonomic treatment
P. trimera (Oliv.) Burkill distributes in the high land areas in Khanh Hoa, Lam Dong provinces of Vietnam. P. trimera is scrambling shrub or erect, long, and curved spines, non-hairy stem. Leaves simple, typical narrow oblong, lamina 1.0–1.5 cm wide, 5–12 cm long; short petiole 0.5 cm long, leaf sub-vein 8–10 pairs; inflorescences axillary, fasciculate, peduncle 3–4 mm long, separate; calyx 3 lobes, 4 mm long; corolla 3; stamens 5, separate; ovaries 3, only 1 ovule, 2 locules in the ovary; globose fruit, 1.5–2.5 cm in diameter, 2 seeded. flowering time from May-Aug., fruiting Sep-Dec. Roots, leaves and stems were used as traditional medicine to treat liver diseases and cancers (Figs. 2, 4a).
Figure 2

The typical morphology and anatomy of Paramignya trimera (Oliv.) Burkill. Woody shrub 1–4 m or above (a); A flowering tree (b); Typical trimerous flowers (c); Green fruits (d); Ripen fruits (d); Opened ripen fruit with two seeds encapsulated by mucus endocarp (e).

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A. buxifolia (Poir.) Oliv. ex Benth distributed mainly in Van Ninh (Khanh Hoa) with several local names such as “Xao cua ga” or “Quyt gai” are medium climbing shrubs, up to 3 m tall; branches grayish brown, branchlets green; spikes axillary 0.5–1.2 cm or sometimes unarmed, apex yellowish; leaves simple, 2.5–3.5 cm wide, 3.5–4.5 mm long, petiole 4–8 mm, leaf blade ovate, obovate, elliptic, glabrous, coriaceous, midvein slightly ridged, apex rounded to obtuse at tip; inflorescences axillary, 1 to several flowers. Flowers 5 merous, petals white, 3–4 mm, stamens 10, calyx persistent. Fruit bluish black when ripe, globose, slightly oblate, or subellipsoid, 7–10 mm in diam., smooth, 1 or 2 seeded. Flowering from May-Aug., fruiting Sep-Dec. Roots, leaves and stems were used as traditional medicine to treat cough, lung diseases and kidney disorders (Fig. 4b).
S. monophylla (Lour.) Tanaka found in Don Duong (Lam Dong) was thorny shrub or small tree; spikes axillary 1–1.5 cm; leaves simple, ovate, apex round or retuse at tip, coriaceous, glabrous, round at base, short petiole; Inflorescences 4–6-flowered; calyx ca. 3.5–5 mm long; petals 4, petals white, oblong, obtuse, glabrous, stamens 8–10; filaments ca. 12 mm long, glabrous; anthers ca. 5 mm long, linear; ovary ca. 2.5 × 1.5 mm, long-ovoid, glabrous, 3-locular; style ca. 7 mm long, continuous with ovary, cylindric, glandular, glabrous; stigma capitate ca. 2.5 mm broad, glandular. Fruits yellow to orange, globose 1.5–2.0 cm in diameter, 1–2 seeded; flowering time from May-Aug., fruiting Sep-Dec. This species was used effectively for cough, expectorant, fever, anti-inflammatory, sciatica treatment and prevent aging of skin cells, roots and leaves used for skin disease, burning leaves to kill mosquitoes and insects (Fig. 2c).
L. scandens (Roxb.), Wight was discovered in Lam Dong of Vietnam with the local name “Xao leo”. L. scandens is woody climber or scrambling shrub; rough tufted from the ground with strong axillary sharp straight or slightly recurved spines. Leaves compound, digitately trifoliate or bifoliolate or simple; petioles 2–6 cm long, glabrous; lamina ca. 6.0–18.0 × 2.5–4.0 cm, variable, oblong-elliptic or oblanceolate, cuneate at base, shortly acuminate at apex, coriaceous, glabrous; secondary nerves 15 pairs; branches brown puberulent. No information from flowering time has been described. According to traditional experience, this plant is used to treat rheumatism, liver disease and ascites (Fig. 2d).
Phylogenetic relation analysis
The phylogenetic tree from ITS sequences included 3 groups (Fig. 5a). The first monophyletic group was only S. monophylla (PC.DD) as an out group. The second monophyletic group included 2 accessions of L. scandens (PR.DL and PR.CT). The third group was paraphyletic group with 9 accessions clustered in 2 sub-groups. The first sub-group included only P. trimera, whereas the second sub-group included 3 accessions P. trimera nested with P. confertifolia and A. buxifolia. In addition, in the second sub-group, the accessions of P. trimera collected in Dien Khanh, Vietnam (PT1.DK) and P. confertifolia from Mensong, China were in the same monophyletic clade whereas A. buxifolia (PA.VN) was clearly separated from others.
The unrooted tree from matK sequences included 3 groups in which the first monophyletic group were 2 species P. lobata and P. scandens (Australia), the second monophyletic group included only P. confertifolia (China) and the third group (paraphyletic group) included 3 sub-groups (Fig. 5b). The first sub-group included all accessions of P. trimera, the second sub-group included only S. monophylla and the third sub-group included L. scandens and A. buxifolia.
The unrooted tree from rbcL sequences included 2 main groups in which the first group included 3 species P. scandens, P. monophylla and P. lobata (Australia) and the second group (paraphilic group) included 5 species P. trimera, P. confertifolia (China), S. monophylla (Japan), A. buxifolia, and L. scandens (Fig. 5c). In this group, some accessions of P. trimera were nested in the paraphylic sub-groups because they did not share an immediate common ancestor.
The pattern of the phylogenetic tree constructed from the concatenated sequences was similar to that of ITS sequences (Fig. 5d). The tree included one monophyletic group with only L. scandens and one paraphyletic group with the accessions of P. trimera nested within P. confertifolia, A. buxifolia and S. monophylla.
Genetic distance analysis
The overall genetic distances for ITS, matK, rbcL and concatenated sequences were 0.11 ± 0.01, 0.29 ± 0.02, rbcL 0.48 ± 0.05 and 0.05 ± 0.0, respectively (Table 2). An overlap between the maximum intraspecific distances and the minimum interspecific distances were observed in the cases of ITS, rbcL and concatenated sequences (Table 2, Fig. 6a,c,d). In case of matK, a clear barcode gap was found between the maximum intraspecific distance (0.0028) and the minimum interspecific distance (0.0056). The histogram and ranked pairwise (K2P) distances demonstrated a significant difference in the cases of matK and rbcL (Fig. 6b,c).
Table 2 Intraspecific and interspecific distances across all data.
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