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Study site, field survey, and in situ filtration
The field survey was performed in Tateyama Bay (34° 60′ N, 139° 48′ E), central Japan, in the proximity of the Kuroshio warm current facing the Pacific Ocean (Fig. 1). This area has many artificial reefs (ARs) created to improve fishing efficiency for fishers. Among the ARs, we focused on one high-rise steel AR (AR1), with a height of 30 m, where fish tended to aggregate (Fig. 1 and S1). Sampling stations were set up at the AR1 and at six linear distant points extending northeast and southwest. These stations were named E150, E500, E750, W150, W500, and W750, where “W” or “E” and the number of each station name represented northeast or southwest and distance in meters from the AR1, respectively (Table S1 and Fig. 1). Another station was set up at a second AR (AR2: 25 m height) 220 m from AR1 because we found AR2 by chance during the survey (Table S1 and Fig. 1), and it might affect the eDNA concentration at other stations.Figure 1(a) Location of sampling stations, cruise track, and a set net in Tateyama Bay. Gray areas indicate landmasses, a gray bold line indicates cruise track, and gray thin lines indicate depth contours with an interval of 20 m. The maps were created using ArcGIS Software 10.6.0.8321 by ESRI (https://www.esri.com/) based on the municipal boundary data of Japan (Esri Japan) and Global Map Japan (Geospatial information Authority of Japan) as well as the M7000-series isobath data set (Japan Hydrographic Association). A picture of the artificial reef (AR1) (b) taken one year after this survey (June 2019) and pictures of the dominant species, (c) splendid alfonsino (Beryx splendens), (d) chicken grunt (Parapristipoma trilineatum), (e) chub mackerel (Scomber japonicus), (f) red seabream (Pagrus major), and (g) jack mackerel (Trachurus japonicus). Photograph credits: (b) Nariaki Inoue, (c) Fumie Yamaguchi, (d, e, g) Yutaro Kawano, and (f) Masaaki Sato.Full size imageWe conducted water sampling at eight stations for eDNA analysis and performed an acoustic survey for estimating relative fish density using research vessel Takamaru (Japan Fisheries Research and Education Agency: FRA) on May 23, 2018. We started the echo sounder survey at the eastern part of the bay and continued it during the water sampling (Fig. 1). Although the echo sounder survey could not differentiate between fish species, we collected this data to assess the association between the estimated concentration of fish eDNA and the echo intensity measured by the echo sounder. Water sampling began at E750, then continued along the transect line to E150, AR1, W150, W500, W750, before going back to AR2. At each sampling station, we collected 10 L of seawater from both the middle and bottom layers by one cast of two Niskin water samplers (5L × 2 samples) and measured vertical profiles of water temperature and salinity with a conductivity-temperature-depth sensor (RINKO profiler, JFE Advantech Co., Ltd.). We subsampled 2L seawater from the 5 L seawater of Niskin sampler using measuring bottle and remaining 3 L seawater was used for pre-wash of measuring bottle and filtration devices. Two 2L samples were collected from two Niskin water samples, and then immediately filtered using a combination of Sterivex filter cartridges (nominal pore size = 0.45 μm; Merck Millipore) through an aspirator (i.e., the two filters were subsets of a single water collection) in a laboratory on the research vessel. After filtration (average time of 15 min), an outlet port of the filter cartridge was sealed with an outlet luer cap, 1.5 ml RNAlater (Thermo Fisher Scientific Inc., Waltham, MA) was injected into the cartridge using a filtered pipette tip to prevent eDNA degradation, and an inlet port was also sealed with an inlet luer cap14. The Niskin water samplers were bleached before each water collection using a commercial bleach solution while filtering devices (i.e., filter funnels and measuring cups used for filtration) were bleached after every filtration. We filtered 2L MilliQ water with a filter funnel and measuring cup as a field negative control to test for possible contamination. The filter cartridges were placed in a freezer immediately after filtration until eDNA extraction. In total we collected and filtered 32 eDNA samples (eight stations × two depth layers × two replicates). Disposable latex or nitrile gloves were worn during sampling and replaced between each sampling station.DNA extraction and purificationWorkspaces were sterilized prior to DNA extraction using 10% commercial bleach, and filter tip pipettes were used to safeguard against cross-contamination. Following the method developed by Miya et al.15, the eDNA was extracted and purified. Briefly, after removing RNAlater inside the cartridge using a centrifuge, proteinase-K solution was injected into the cartridge from the inlet port, and the port was re-capped with the inlet lure cap. The eDNA captured on the filter membrane was extracted by constant stirring of the cartridge at a speed of 20 rpm using a roller shaker placed in an incubator heated at 56 °C for 20 min. The eDNA extracts were transferred to a 2-ml tube from the inlet of the filter cartridges by centrifugation. The collected DNA was purified using a DNeasy Blood & Tissue Kit (Qiagen) following the manufacturer’s protocol. After the purification, DNA was eluted using 100 μl of the elution buffer (buffer AE). All DNA extracts were frozen at − 20 °C until paired-end library preparation.Preparation of internal standard DNAsFive artificially designed and synthetic internal standard DNAs, which were similar but not identical to the region of any existing fish mitochondrial 12S rRNA, were included in the library preparation process to estimate the number of fish DNA copies [i.e., quantitative MiSeq sequencing (qMiseq)]7,16. They were designed to have the MiFish primer‐binding regions as those of known existing fishes and to have the conserved regions in the insert region. Variable regions in the insert region were replaced with random bases so that no known existing fish sequences had the same sequences as the standard sequences. The standard DNA size distribution of the library was estimated using an Agilent 2100 BioAnalyzer (Agilent, Santa Clara, CA, USA), and the concentration of double-stranded DNA of the library was quantified using a Qubit dsDNA HS assay kit and a Qubit fluorometer (Thermo Fisher Scientific Inc., Waltham, MA, USA). Based on the quantification values obtained using the Qubit fluorometer, the copy number of the standard DNAs was adjusted as follows: Std. A (100 copies/µl), Std. B (50 copies/µl), Std. C (25 copies/µl), Std. D (12.5 copies/µl) and Std. E (2.5 copies/µl). Then, these standard DNAs were mixed.Paired-end library preparationTwo PCR‐level negative controls (i.e., each with and without internal standard DNAs) were employed for MiSeq run to monitor contamination during the experiments. The first-round PCR (1st PCR) was carried out with a 12-µl reaction volume containing 6.0 µl of 2 × KAPA HiFi HotStart ReadyMix (Roche, Basel, Switzerland), 0.7 µl of each primer (5 µM), 2.6 µl of sterilized distilled H2O, 1.0 µl of standard DNA mix and 1.0 µl of template. Note that the standard DNA mix was included for each sample. The final concentration of each primer was 0.3 µM. We used a mixture of the following four PCR primers modified from original MiFish primers16: MiFish-U-forward (5′-ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT NNN NNG TCG GTA AAA CTC GTG CCA GC-3′) and MiFish-U-reverse (5′-GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATC TNN NNN CAT AGT GGG GTA TCT AAT CCC AGT TTG-3′), MiFish-E-forward (5′-ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT NNN NNG TTG GTA AAT CTC GTG CCA GC-3′), and MiFish-E-reverse (5′-GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATC TNN NNN CAT AGT GGG GTA TCT AAT CCT AGT TTG-3′). These primer pairs co-amplify a hypervariable region of the fish mitochondrial 12S rRNA gene (around 172 bp) and append primer-binding sites (5′ ends of the sequences before five Ns) for sequencing at both ends of the amplicon. The five random bases were used to enhance cluster separation on the flow cells during initial base call calibrations on the MiSeq platform. The thermal cycle profile after an initial 3 min denaturation at 95 (^circ)C was as follows (35 cycles): denaturation at 98 (^circ)C for 20 s; annealing at 65 (^circ)C for 15 s; and extension at 72 (^circ)C for 15 s, with a final extension at the same temperature for 5 min. Eight replications were performed for the 1st PCR, and the replicates were pooled to minimize the PCR dropouts. The 1st PCR products from the eight tubes were pooled in a single 1.5-ml tube. Then, we sent the 1st PCR products to IDEA consultants, Inc. to outsource the following MiSeq sequencing processes. The pooled products were purified and size-selected for 200–400 bp using a SPRIselect (Beckman Coulter, Inc.) to remove dimers and monomers following the manufacturer’s protocol.The second-round PCR (2nd PCR) was carried out with a 24 µl reaction volume containing 12 µl of 2 × KAPA HiFi HotStart ReadyMix, 2.8 µl of each primer (5 µM), 4.4 µl of sterilized distilled H2O, and 2.0 µl of template. We used the following two primers to append the dual-index sequences (8 nucleotides indicated by Xs) and flowcell-binding sites for the MiSeq platform (5′ ends of the sequences before eight Xs): 2nd-PCR-forward (5′-AAT GAT ACG GCG ACC ACC GAG ATC TAC ACX XXX XXX XAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC T-3′); and 2nd- PCR-reverse (5′-CAA GCA GAA GAC GGC ATA CGA GAT XXX XXX XXG TGA CTG GAG TTC AGA CGT GTG CTC TTC CGA TCT-3′). The thermal cycle profile after an initial 3 min denaturation at 95 (^circ)C was as follows (12 cycles): denaturation at 98 (^circ)C for 20 s; combined annealing and extension at 72 (^circ)C for 15 s, with a final extension at 72 (^circ)C for 5 min. The concentration of each second PCR product was measured by quantitative PCR using TB Green Fast qPCR Mix (Takara inc.). Each sample was diluted to a fixed concentration and combined (i.e., one pooled 2nd PCR product that included all samples). The pooled 2nd PCR product was size-selected to approximately 370 bp using BluePippin (Sage Science). The size-selected library was purified using the Agencourt AMPure XP beads, adjusted to 4 nM by quantitative PCR using TB Green Fast qPCR Mix (Takara Bio Inc.), and sequenced on the MiSeq platform using a MiSeq v2 Reagent Kit (2 × 150 bp) (Illumina, Inc.).Data preprocessing and taxonomic assignmentThe raw MiSeq data were converted into FASTQ files using the bcl2fastq program provided by Illumina (bcl2fastq v2.18). The FASTQ files were then demultiplexed using the command implemented in Claident17. We adopted this process rather than using FASTQ files demultiplexed by the Illumina MiSeq default program in order to remove sequences with low-quality scores and PCR artifacts (chimeras).The processed reads were subjected to a BLASTN search against the full NCBI database. We excluded unique sequences of the following settings: the sequence belonged to organisms other than bony fishes, sharks, and rays; the sequence similarity between queries and the top BLASTN hit was  More

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Indigenous territories, long a bulwark against deforestation in the Amazon, are under increasing threat in Brazil, according to an analysis of 36 years’ worth of satellite imagery. The data show that illicit mining operations on Indigenous lands and in other areas formally protected by law have hit a record high in the past few years, under the administration of President Jair Bolsonaro, underscoring fears that his policies and rhetoric are undermining both human rights and environmental protection across the world’s largest rainforest. These operations strip the land of vegetation and pollute waterways with mercury.
When will the Amazon hit a tipping point?
The analysis, released in late August, comes as scientists and environmentalists warn of a deteriorating situation in Brazil; Indigenous groups have frequently found themselves in violent clashes with miners since Bolsonaro took office in 2019 — and they are demanding more protection for their land. Although Indigenous territories are legally protected, Bolsonaro has openly called for mining and other development in them.“This is definitely the worst it’s been for Indigenous peoples since the constitution was signed in 1988,” says Glenn Shepard, an anthropologist with the Emílio Goeldi Museum in Belém. Before this, Brazil was ruled by a military dictatorship.Researchers at MapBiomas, a consortium of academic, business and non-governmental organizations that has been conducting geospatial studies across Brazil, developed algorithms that they used in conjunction with Google Earth Engine to conduct the analysis. After training the algorithms on images of mining operations — desolate landscapes where forests have been converted into a collection of sand dunes pockmarked by mining ponds — the team ran its analysis on a freely available archive of imagery captured by the US Landsat programme, and then analysed trends on Indigenous lands and other formally protected areas where mining is not allowed.Over the past decade, illegal mining incursions — mostly small-scale gold extraction operations — have increased fivefold on Indigenous lands and threefold in other protected areas of Brazil such as parks, the data show (see ‘Mining incursions’). The findings agree broadly with reports from Brazil’s National Institute for Space Research (INPE) in São José dos Campos, which monitors the country’s forests and has been issuing alerts about mining incursions for several years. “We kind of knew that this was happening, but to see numbers like this is scary even for us,” says Cesar Diniz, a geologist with the geospatial-analysis company Solved in Belém, Brazil, who led the analysis for MapBiomas.Clashes on multiple frontsAside from being home to their people, Indigenous territories play a part in protecting the Amazon’s biodiversity and the enormous pool of carbon that is locked away in its trees and soils. Numerous studies have found that Indigenous lands, as well as other conservation areas, are effective buffers against tropical deforestation in the Amazon1,2, which is responsible for around 8% of global carbon emissions.Earlier this month, the International Union for Conservation of Nature (IUCN) approved a motion, put forward by Indigenous groups, calling on governments to protect 80% of the Amazon basin by 2025. Indigenous representatives say they plan to fight for implementation across the Amazon, but the proposal faces a particularly tough sell in Brazil under Bolsonaro, whose pro-business conservative government has scaled back enforcement of existing environmental laws and halted efforts to demarcate new Indigenous territories.

Sources: MapBiomas/Amazon Geo-Referenced Socio-Environmental Information Network/Terrabrasilis

Indigenous groups have also taken their case to the International Criminal Court in The Hague, the Netherlands. On 9 August, the Articulation of Indigenous Peoples of Brazil (APIB), which represents Indigenous groups across the country, filed a complaint with the court accusing the Bolsonaro administration of violating human rights and, they claim, paving a path for genocide by undermining Indigenous rights, reducing environmental protections and inciting incursions and violence through calls for mining and land development. APIB also made it clear that it’s not just Indigenous rights at stake, drawing a direct link between the protection of their territories and of the globe.

Members of the Munduruku people sit in front of equipment from an illegal mining operation on their land.Credit: Meridith Kohut/The New York Times/eyevine

“Defending the traditional territories of Amazonian communities is the best way to save the forest,” says Luiz Eloy Terena, an anthropologist and lawyer from the village of Ipegue who coordinates legal affairs for APIB. “What is needed is a state commitment on the demarcation and protection of Indigenous lands, which are the last barrier against deforestation and forest degradation.”During an address to the United Nations General Assembly on 21 September, Bolsonaro said he was committed to protecting the Amazon and emphasized that 600,000 Indigenous people live “in freedom” on reserves totalling 1.1 million square kilometres of land, equivalent to 14% of Brazil’s territory. In the past, Bolsonaro has publicly said that Indigenous peoples have too much land given their sparse population, and at times called for their “integration”. The Bolsonaro administration did not respond to Nature’s requests for comment regarding illegal mining in the Amazon, its Indigenous and environmental policies or the accusations filed with the International Criminal Court.Existential threatBrazil earned recognition as a leader in sustainable development during the 2000s. Former president Luiz Inácio ‘Lula’ da Silva and his Workers’ Party put in place policies that helped to curb deforestation in the Amazon by more than 80% between 2004 and 2012.

Source: Brazilian National Institute for Space Research

But the party was dogged by corruption charges that would later land Lula in jail, and its environmental agenda ultimately faltered. In 2012, the increasingly conservative Brazilian Congress weakened a once-vaunted forest-protection law. With each successive government, funding for the country’s main environmental enforcement agency, the Institute of Environment and Renewable Natural Resources (IBAMA), has decreased: IBAMA had 1,500 enforcement agents in 2012, compared with just 600 today, says Suely Araújo, a political scientist in Brasília who spent nearly three decades working in the Brazilian Congress and led IBAMA from 2016 to 2018.The rate of deforestation in the Amazon, which includes land converted for mining, agriculture and other development, began rising anew after 2012 and shot up by 44% during Bolsonaro’s first two years in office, according to INPE (see ‘Razing the rainforest’). Many expect yet another increase when the numbers for 2021 are released later this year.But the biggest threats are yet to come, says Araújo. The current government is now pushing legislation in Congress — as well as arguments in a case that is pending before Brazil’s Supreme Court — that would make it harder to establish new Indigenous lands and could even allow the government to repossess existing lands. Other legislation that has been advanced by Bolsonaro’s supporters in Congress would open up Indigenous lands to industrial development, grant amnesty to people who have illegally invaded public lands and gut regulations governing major infrastructure projects such as mines, roads and dams.
The scientists restoring a gold-mining disaster zone in the Peruvian Amazon
“It’s painful,” says Araújo, who decided to forgo retirement and join Brazil’s Climate Observatory, a coalition of activist and academic groups fighting to preserve the country’s social and environmental protections. “This has become my mission.”For Indigenous tribes, the growing damage to their lands and the rainforest pose an existential threat. More than 6,000 Indigenous people descended on Brasília, the country’s capital, in August and September in protest against Bolsonaro’s policies on land demarcation and the environment. They also travelled to Marseille, France, for the IUCN’s World Conservation Congress earlier this month to promote their motion to protect the Amazon basin.“We will not give up,” says José Gregorio Diaz Mirabal, a member of the Wakueni Kurripaco people of Venezuela and the elected leader of the Congress of Indigenous Organizations of the Amazon Basin. “Science supports us, and the world is waking up.”

doi: https://doi.org/10.1038/d41586-021-02644-x

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