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50 protocols using cellulose nitrate filter

1

Cultivation and Transformation of Candida albicans

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Candida albicans SC5314 (Gillum, Tsay and Kirsch 1984 (link)) was grown on YPD agar plates (1% yeast extract, 2% Bacto-peptone, 2% glucose and 1.5% agar) for 18 h at 37°C. Yeast cells were harvested from colonies using sterilized scrapers and washed with phosphate buffered saline (PBS) using sterilized cellulose nitrate filters (1.2 μm pore size, Sartorius-Stedim, Gottingen, Germany). To obtain mycelia, 5 × 106 yeast cells of C. albicans were inoculated in 50 mL of 20% fetal bovine serum medium in a disposable plate, then incubated for 24 h at 37°C. Mycelia were harvested and washed with PBS using sterilized cellulose nitrate filters (8 μm pore size, Sartorius-Stedim, Gottingen, Germany). Cells of each type were separately pooled at −80°C to be crushed physically.
C. albicans expressing green fluorescent protein (GFP) was constructed using the plasmid pGFP-ACT1 (Umeyama et al.2005 (link)) linearized with StuI, which was introduced into the CaRP10 locus of C. albicans ura-strain CAI4. Yeast cells were transformed by the modified lithium acetate method of Umeyama et al. (2005 (link)). This strain was used for experiments in vivo because it is possible to confirm inoculum cells easily.
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2

Microbial Community Analysis of Biodegradation

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Eighty milliliters of the water enriched with microorganisms used for the biodegradation tests was filtered (0.2μm porosity, cellulose nitrate filters, Sartorius Stedim). The filters were then ground in liquid nitrogen to a fine powder, and DNA was extracted using the Mobio-Power Soil DNA isolation kit (Mobio Laboratories, Carlsbad, CA) in line with the supplier’s recommendations. The genomic DNA was sent to a commercial company (MR DNA, Shallowater, Texas, United States). Following the amplification of the V4 hypervariable region of the 16S rRNA gene (PCR primers 515/806), the amplicons were sequenced via MiSeq 2 × 300bp sequencing (Illumina, California, United States) in line with the supplier’s recommendations. The sequences were converted and demultiplexed with QIIME1. The sequences were analyzed using the software package DADA2 (Callahan et al., 2016 (link)) in the QIIME2 pipeline. With this package, the sequences were treated by quality filtering, merging, dereplicating, and removing chimeras to determine amplicon sequence variants (ASVs). Taxonomy was assigned using VSearch (Rognes et al., 2016 (link)) against the SILVA SSU 138 NR database (Quast et al., 2013 (link)) without uncultured/environmental sequences. The raw data were deposited in the NCBI SRA under bioproject ID PRJNA739070.
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3

Isolation of Bacterial Communities from Caulerpa compressa

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Bacterial communities were collected from submerged thalli of C. compressa and the surrounding seawater six times from May to October 2014 during the vegetative growth season (Table S1). Each time, epiphytic bacteria were collected from 3 randomly selected thalli of C. compressa. Sterile cotton swabs on wooden sticks (Aptaca) were used to rub approximately 12 cm2 of surface from the perennial base to the tip of primary branches. Swabs were immediately placed in sterile 1.5 ml Eppendorf tubes. Thalli that were overgrown with epiphytic seaweeds or animals were avoided. To compare the bacterial communities that grow on C. compressa with those present in the surrounding environment, two samples (n = 2) of seawater (500 ml) were randomly collected each time using black polyethylene bottles (Kartell). Seawater samples were filtered in the field with an electric vacuum pump, connected to a portable electric generator, first onto 3.0 μm pore size cellulose acetate filters (Millipore), to remove most eukaryotes, and then onto 0.2 μm pore size cellulose nitrate filters (Sartorius) to retain the bacteria. Samples were transported on ice to the lab and stored at −80°C until DNA extraction.
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4

eDNA Detection in Green Crabs

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A water filtration system with four 300 mL filtration funnels and sterile 0.45 µm cellulose nitrate filters (Sartorius, Germany; #11,306–47-ACN) connected to a vacuum pump (Gast DOA-P7004-AA) was constructed (see Additional file 1: Fig. S1). In a lightproof box a 7 W UV light was used to sterilize the filtration setup for 10 min before each water filtration. After water samples were filtered, filters were stored in individual sterile 2 mL Eppendorf tubes at −80 ℃ until DNA isolation.
For determinations on the minimum volume of water that could be collected and filtered to test for the presence of eDNA from C. maenas, water was sampled from a 500 L tank containing more than 100 green crabs in six volumes (100, 200, 300, 400, 500, and 600 mL, n = 3 per volume). This water was filtered and eDNA was isolated using the Qiagen DNeasy Blood and Tissue Kit. DNA was amplified using the designed primers and TaqMan probe sequence for qPCR, and total DNA concentration was measured using a ThermoFisher NanoDrop™ spectrophotometer.
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5

N-CD Protein Purification by IMAC

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The N-CD protein was purified by metal affinity chromatography (IMAC) using a XK-16/20 column (GE Healthcare, Uppsala, Sweden) packed with Ni-NTA agarose matrix (Qiagen, Valencia, USA) in an AKTATM pure system (GE Healthcare). The cell culture supernatant containing the N-CD protein was clarified by centrifugation at 4300 g for 10 minutes at 4°C and filtrated through 0.45 μm and 0.2 μm cellulose nitrate filters (Sartorius). Afterward, it was equilibrated to a final concentration of 300 mM NaCl, 50 mM NaH2PO4 and 10 mM imidazole (equilibrium buffer) and the pH was adjusted to 7.4. The matrix was equilibrated with 5 column volumes (CV) and the supernatant was loaded onto the column overnight at 0.5 mL/min at 4°C. A wash with 10 CV of 300 mM NaCl, 50 mM NaH2PO4 and 20 mM imidazole, pH 7.4. The elution was done using 5 CV of 300 mM NaCl, 50 mM NaH2PO4 and 250 mM imidazole, pH 7.4. After purification, a buffer exchange to PBS was done with a PD10 desalting column (GE Healthcare, New York, USA). Protein was concentrated six-fold using Amicon® centrifugal filter units 10K (Millipore, Tullagreen, Ireland). Purified protein was quantified by ELISA as described before.
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6

Optimized EPS Production from Bacterial Fermentation

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The MRS-sucrose medium was used for EPS production and contain: 4% (w/v) sucrose, 10 g/L tryptone, 10 g/L meat extract, 5 g/L yeast extract, 5 g/L sodium acetate, 2 g/L disodium phosphate, 2 g/L tri-ammonium citrate, 0.1 g/L MgSO4, and 0.05 g/L MnSO4 (pH 6.5) [31 (link), 32 ]. The medium was autoclaved at 121°C for 15 min. The fermentation temperature, inoculum size, and fermentation time were 30°C, 3.0% (v/v), and 24 h, respectively. After incubation, bacterial cells were separated from the EPS preparation by centrifugation (5,000 rpm for 10 min at 4°C) of the culture broth. The supernatant, containing the EPS fraction, was filtered under vacuum through Sartorius cellulose nitrate filters of (0.45 μm pore size) to eliminate cells and large cellular. The obtained supernatant was divided into two batches for the purification step.
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7

Air Sampling of Microbial Diversity

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Air samples were collected by impaction with a single-stage air sampler Microflow α (AQUARIA srl, Italy), holding 380 jets with a diameter of 1 mm. The sampler was placed in a central position of the cave at 1 m height. The impaction flow rate was set at 120 L min−1, and the airstream was directed on 90-mm-diameter agar Petri dishes containing different growth media, mainly Lysogeny Broth Agar (LBA) (10 g L−1 NaCl (Sigma-Aldrich, USA), 5 g L−1 yeast extract (Merck, Germany), 15 g L−1 agar (Difco, Michigan) and Plate Count Agar (PCA) (Difco, Michigan), or on cellulose nitrate filters with a pore size of 0.45 µm (Sartorius, Germany). Different sampling volumes, between 250 and 1000 L, were collected in duplicate. Filters were stored at −20 °C in sterile tubes until genomic DNA extraction.
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8

Contaminant-Free Aquatic Sample Preparation

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Sodium Chloride, Hydrogen Peroxide solution 30%, and Potassium hydroxide were provided by Carlo Erba (Val De Reuil, France). Cellulose nitrate filters (pore size 8 μm) and cellulose acetate filter (pore size 0.45 μm) were purchased from Sartorius Stedim Biotech (Gottingen, Germany). The filtrating system was provided by Advantec (Dublin, CA 94568, USA).
As contamination precaution, all of the liquid (freshwater, saltwater, and hydrogen peroxide) was filtered with 0.45 μm cellulose acetate filter before use. All containers and beakers were rinsed three times with filter water before use to avoid contamination. Samples were covered by foil paper during digestion and when not in use. Filters were covered with glass lids during observation under a stereomicroscope (Zeiss 47 50 22 West Germany Microscope).
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9

Aqueous Sample Preparation for Analytical Analysis

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Aqueous samples were prepared following the method of Kovačič et al. (2019) [17 (link)]. All samples were defrosted overnight and then filtered sequentially through glass fiber (MN GF-2, Machery—Nagel, Dueren, Germany) and cellulose nitrate filters (0.45 μm, Sartorius, Göttingen, Germany) to prevent clogging of the solid-phase extraction (SPE) cartridges. In the case of the aqueous sludge phase, the samples were filtered using MN GF-4 filters. The filtered samples (250 mL) were then spiked with 25 μL of the internal standard mixture 13C12-BPS, 13C12-BPF, 13C12- BPB, BPA-d16 (c = 1 μg mL−1), and 500 μL of concentrated HCl were added. The samples were loaded onto Oasis Prime HLB cartridges (60 mg, 3 mL; Waters, Massachusetts, USA) at a flow rate of 3 mL min−1. After loading, the sorbents were washed with 3 mL of 10% MeOH in water and dried under vacuum (−1.33 kPa) for 45 min. The elution step was performed using 5% FA in EtAc (3 × 0.6 mL). The solvent was evaporated under nitrogen at 40 °C.
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10

Environmental DNA Extraction and Quantification

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The environmental DNA was extracted from cellulose nitrate filters with 0.2 μm porous size (Sartorius, Germany) using the Powerwater kit (Qiagen, Netherlands) per the Manufacturer’s protocol. DNA concentrations were measured using the NanoDrop-1000 spectrophotometer (Nanodrop Technologies, USA) and where applicable, the DNA concentrations were diluted to 20 ng/μL for downstream applications.
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