Spider and silk collection
Golden orb spiders Trichonephila clavata (Koch, 1878) of the family Araneida are widely distributed in low and mid-elevation mountainous areas in Taiwan. While most members of the family Nephilidae are solitary, T. clavata aggregate together using communal scaffold silks and deposit lots of prey remains on webs33. Spiders were collected from Wushiken, Taichung City, Taiwan and were individually housed in enclosures at Tunghai University. We followed the method reported in Blamires et al. (2012) to collect bundles of MA silks (5 mg each sample) directly from large females through forcible extraction using an electric rotor with a reeling rate of 0.01 m/sec. Bundles of MA silk samples were later used for transmitted electron microscopy (TEM) and nuclear magnetic resonance analyses (NMR)34.
Isolation and culture of bacteria from spiders and webs
Bacterial strains were isolated and identified from the webs of T. clavata. Webs including prey remains were collected from the field and were placed into sterile plastic ziplock bags and later liquefied followed by vortexing before being spread on sterile agar plates. Agar plates receiving the aforementioned treatments were then subjected to standard bacterial isolation and culture processes. For each colony of bacteria 16S ribosomal DNA was amplified, sequenced using PCR, and compared to known sequences using BLAST. A total of 22 strains of bacteria were isolated and among them Microbacteriums sp. (Max. score = 2704, identity = 100%, Accession number JQ793425.1) and Novosphigobium sp. (Max. score = 2590, identity = 97.3%, Accession number KF465976.1) were discovered through BLAST identification. These two bacteria were suspended in 5 ml of full nutrient broth and incubated for 24 h at 27°C. We then added 20% glycerol to the tubes, and stored them at − 80°C. The bacterial strains in this study were deposited in the Microbial Ecology Laboratory, Department of Life Science, Tunghai University, Taiwan.
Visualization of T. clavata MA silk surface layers
We used transmission electron microscopy (TEM) to visualize various surface layers of MA silks produced by T. clavata. MA silk sample was fixed in Karnovsky solution at 4℃ and washed with 0.1M Cacodylate buffer 10 minutes thrice and postfixed in 1% OsO4 for 30 minutes at room temperature. After being postfixed, the pieces were washed thrice in Cacodylate buffer for 10 minutes. The samples were dehydrated in 50% EtOH for 10 minutes, moved to a new Eppendorf, and after centrifugation the supernatant was removed. Samples were dehydrated with 75% EtOH (10 minutes), 95% EtOH (10 minutes), and then 100% EtOH (10 minutes for three times). Samples were then transferred to 1,2-propylene oxide/EtOH mixture (1:3, 1:1, 3:1) for 15 minutes. Subsequently the samples were rinsed with 100% propylene for ten minutes trice and placed in Epon/propylene oxide mixture (1:3, 1:1, 3:1) for 1 hour, 4 hours, and 8 hours and then 100% Epon for 12 hours. Finally, samples were embedded in a fresh Eppendorf with fresh Epon at 40℃ for 18 hours and 60℃ for 24 hours. Samples were cut by using ultramicrotome (Leica Ultracut UC7, Wetzlar, Germany), and thin sections (80 nm) were stained with uranyl acetate and lead citrate and viewed under a transmission electron microscope (Hitachi HT-7700, Tokyo, Japan).
Manipulation of T. clavata MA silk surface layers
We followed the protocols reported by Sponner et al. (2007) and Yazawa et al. (2019) to remove lipid and glycoprotein layers of MA silks17, 23. To remove lipid layer, about 5 mg of MA silk samples was submerged in diethyl ether and shaken gently for 10 minutes. After such operation, the silk samples were rinsed in distilled water then the diethyl ether treatment was repeated again. To remove glycoprotein layer, silk samples receiving lipid removal treatment was placed in Eppendorf containing 0.1% Triton-X-100 and vortexed vigorously for 10 minutes and such process was repeated for 10 times. Silk samples with lipid and glycoprotein layers removed were examined by NMR to verify the effectiveness of treatments. Treated silk samples were placed in Eppendorf tubes and were added 1 mL of 1,1,1,3,3,3-Hexafluoro-2-propanol-d2. Subsequently, 0.5 ml of the resulting solution was extracted from the tube and used for measurement and analysis. The 1H NMR spectra of dissolved silk bundles were recorded using a Bruker AVIII HD 400 spectrometer (Bruker Taiwan co., Hsinchu, Taiwan). Chemical shifts were reported in ppm downfield from (CH3)4Si, and coupling constants (J ) were given in Hertz. The NMR spectra of silk samples with intact surface layers and those receiving surface layer treatments were compared to see whether the signals associated with silk surface layers were different between them.
Experimental design of silk tensile testing
In this study, we used a multi-factorial design to comprehensively evaluate the effects of bacterial species, silk surface layer and bacterial cultural broth on tensile properties of T. clavata MA silks (Supplementary Fig. 1). Single thread MA silk samples collected from T. clavata were exposed to either Microbacterium sp. or Novosphingobium sp. and mechanical performances of MA silks threads incubated with or without bacteria were compared. Single strand MA silk samples to be exposed to various bacteria were subjected to three surface layer treatments (layers intact, lipid layer removed and glycoprotein removed). Bacteria to be interacted with MA silk samples were cultured in three different broth (no nutrient; minimal nutrient with nitrogen source, without carbon source; minimal nutrient with carbon source, without nitrogen source). We collected 10 mature T. clavata females from the field. From each female spider we collected at least 36 single strand MA silk samples to make sure that they were comprehensively used in all factorial treatments (two bacterial species × two treatments × three surface layer manipulations × three broth types) to minimize the confounding effect that silk samples used in various treatments were collected from different individuals.
Preparation of silk samples for tensile testing
Each female T. clavata spider was placed ventral side up unto a Styrofoam block and was immobilized with non-adhesive tapes and pins. Single strand of MA silk was reeled from spider's anterior spinneret at a speed of 0.01m/sec using a rotor powered by an electric motor. The MA silk strand was collected onto a cardboard with a 10 mm × 10 mm gap. Double sided sticky tape was used to affix the silk thread at each end of the cardboard and PVA waterproof glue (Huayu Enterprise Co., Taipei, Taiwan) was applied latter near the edges of gaps. When the glue dried, we mounted the cardboard on microscope slides and divided silk samples into three groups. In the first group, the surface layers of MA silks were kept intact. In the second group the lipid layer of MA silk samples was removed while in the third group the glycoprotein layer was removed. We removed lipid layer of MA silks mounted on cardboards by dropping diethyl ether directly on the silk thread. After it dried out the silk samples were washed by dripping water. The aforementioned procedures were repeated two times and the silk samples were left to dry for 5 minutes. To remove glycoprotein layer, on half of the silk samples treated with diethyl ether we dripped 0.1% Triton X-100 solution diluted with PBS broth, followed by washing with water. After 15 minutes the aforementioned processes were repeated again for 10 times.
Interaction of MA silk and bacteria
We evaluated the effects of Microbacterium sp. and Novosphingobium sp. isolated from webs of T. clavata on tensile properties of host MA silks. Zhang et al. (2019) showed that most bacteria would not proliferate unless extra nitrogen or carbon nutrients were supplemented16. Therefore, we cultured these two bacteria in three types of broth. In the first one, the PBS broth (phosphate buffer saline, 10 ml 0.5 M KH2PO4 and 2.5 ml 0.4 M MgCl2. 6H2O, with 2 L water), no extra nutrient was supplemented. In the second one, the CFN broth (minimal nutrient without carbon source, 13.6 g KH2PO4, 7.1 g NaHPO4, 0.25 g MgSO4.7H2O, 0.01 g CaCl2 and 5 g (NH4)2SO4), extra nitrogen was supplemented. In the third one, the NFG broth (minimal nutrient without nitrogen source, 13.6 g KH2PO4, 7.1 g NaHPO4, 0.25 g MgSO4.7H2O, 0.01 g CaCl2 and 8 g Glucose, with 1 L water), extra carbon was supplemented. For each bacterium species, 5 µl of bacterial suspension (105–106 cells/ml) was dripped onto the center part of the silk thread mounted on the cardboard, then the silks were incubated at 28℃ for 24 hours. Broth without bacteria was also applied to the silk samples following the same procedures as the control. All operations were carried out under sterile conditions to avoid contamination. The bacteria used in this present study were deposited in Microbial Ecology Laboratory, Tunghai University, Taiwan.
Testing of silk tensile properties
After being subjected to bacterial exposure and incubation, we let samples air dry from extra humidity and broth to exclude its effect on extensibility. Each cardboard with the mounted silk sample was taped to a glass slide and photographed at 100x using a digital camera (Canon EOS 650D, Tokyo, Japan) attached to a polarized light microscope (Olympus BX53, Tokyo, Japan). We measured diameter of each silk samples using Image J program35. Then, we performed mechanical tests for each 10 mm silk sample (within two weeks after the completion of treatments) using a Nano Bionix tensile tester (MTS Systems Corp., Eden Prairie, MN, USA) at the Center for Measurement Standards, Industrial Technology Research Institute, Hsinchu, Taiwan. Silks were stretched at a rate of 1% gauge length per second until rupture to generate the load-extension data. All testing was conducted under controlled ambient temperature and humidity (20℃, 30% RH). Young’s modulus, maximum stress, extensibility (i.e., breaking strain) and toughness were derived from stress-strain curves plotted by the program Test Works 4.0 as described by Piorkowski et al. (2018)36.
Detecting presence of bacterial exopolysaccharide
First, spider silk was reeled manually onto a glass ring to create a web mesh and a total of three such rings were prepared. In the first two silk sings, a few droplets (with a total volume of 5 µl) of either Microbacterium sp. or Novosphingobium sp. cultured in NFG broth were dripped by pipette onto spider silk mesh. In the third ring same amount of NFG broth was dripped on silk mesh to serve as a control. All three rings were then incubated at 28℃ for 24 hours. After incubation, silk form the rings was collected, placed into Eppendorf, weighted, and proceeded to NMR operation. The 1H NMR spectra were recorded using a Bruker AVIII HD 400 spectrometer. Chemical shifts were reported in ppm downfield from (CH3)4Si, and coupling constants (J) were given in Hertz. Spider silk samples (20 mg each) was mixed with D2O and soaked in an Eppendorf tube for 15 minutes. Subsequently, 0.5 ml of the resulting D2O solution was extracted from the tube and used for measurement and analysis.
Statistical analyses
We conducted multivariate analysis to determine the explanatory variable structure and then conducted univariate analyses for each tensile properties according to the same structure. We performed partial redundancy analysis (pRDA) to compare the tensile properties (i.e. maximum strain/stress, toughness and modulus) of MA silk among treatments. Method pRDA, as a multivariate analysis technique, provides the capability to simultaneously model silk properties, assess linear effects and/or interactions, and account for the random effect of spider identity, which is not the primary focus of this study. Without the intentions of interspecific comparisons, we separately performed pRDA for each spider species. We first calculated the averages of each tensile properties obtained from same spider under same treatment to avoid pseudo-replication issue, and then we natural-log transformed all averaged tensile properties to cope with heteroscedasticity. Four tensile properties were assigned as the response variables. The following four explanatory factors were included: bacteria treatment (with/without bacteria), layer type (G/L/N), bacterial species (Microbacterium vs. Novosphingobium) and broth type (CFN/NFG/PBS). Interaction(s) among main factors was included when permutation P (Pperm) was less than 0.1 during a forward stepwise process with permutation test, which shuffled the pRDA residuals within each spider individual. Spider individual identity was also included as the conditioning factor to achieve the comparisons within individual. After variables structure was determined, we performed linear mixed models (LMM) to fit each tensile property with the same RHS structure. To cope with the pseudo-replication issue and achieve comparisons within spider identity, the following two random factors were assigned: spider individual identity and the treatment within spider individual identity, and the data for LMMs were not averaged beforehand. P-values of each parameter among different tensile properties were gathered and adjusted by using the Benjamini-Hochberg method37 to control the false discovery rate (FDR). All of the pRDAs and LMMs were computed by the R package ‘vegan’ v. 2.6–238 and ‘lmerTest’ v. 3.1–339, respectively. All analyses were conducted under the R environment v. 4.2.0.