More stories

  • in

    Analysis of volatiles from feces of released Przewalski’s horse (Equus przewalskii) in Gasterophilus pecorum (Diptera: Gasterophilidae) spawning habitat

    The volatiles from fresh feces of Przewalski’s horse at the pre-oviposition, oviposition, and post-oviposition stages of G. pecorum
    Throughout the stages of pre-oviposition (PREO), oviposition (OVIP), and post-oviposition (POSO) of G. pecorum, 70 volatiles were identified in fresh feces of Przewalski’s horse. Among them, 46, 48, and 52 volatiles were identified at PREO, OVIP, and POSO, respectively, and 29 volatiles were common at all three stages. In addition, 4, 5, and 9 volatiles were common between PREO and OVIP, OVIP and POSO, as well as PREO and POSO, whereas 4, 10, and 9 volatiles were unique at the single stage of PREO, OVIP, and POSO, respectively (Table 1; Fig. S1). According to relative content, the two main chemical classes of volatiles were aromatic hydrocarbons and alkenes, that is, their respective contents in a sample were both more than 25% of the total content. Except alcohols which exhibited significant difference between PREO and POSO (One-way ANOVA, F = 8.400, df = 2, P = 0.018), there was no significant difference in all other pairwise comparisons among the nine chemical classes at three stages (One-way ANOVA or Kruskal–Wallis test: P  > 0.05) (Fig. 1). Non-metric multidimensional scaling (NMDS) analysis revealed certain extent of overlap (Fig. 2), while one-way analysis of similarity (ANOSIM) indicated that there were significant differences among the three stages (R = 0.5391, P = 0.008).Table 1 The volatiles from fresh feces of Przewalski’s horse at the stages of PREO, OVIP, and POSO of Gasterophilus pecorum.Full size tableFigure 1Volatile classes detected from fresh feces of Przewalski’s horse at the stages of PREO, OVIP, and POSO of Gasterophilus pecorum. PREO, OVIP, and POSO represent fresh feces at the stages of pre-oviposition, oviposition, and post-oviposition of Gasterophilus pecorum, respectively. Data are mean (n = 3) ± SE. Different letters indicate significant differences at P  0.05). Furthermore, acetic acid was common to PREO and POSO, but no difference was observed between them (Independent t test, t = 0.137, df = 4, P = 0.897) (Table 1).Of particular concern among the eight volatiles mentioned above, ammonium acetate and butanoic acid were unique to OVIP, the critical stage of oviposition. Although not one of the five most abundant volatiles, another nine volatiles were also specific to OVIP, of which hexanoic acid, cyclopentasiloxane,decamethyl- and cyclohexene,3-methyl-6-(1-methylethyl)- were higher than 1% in relative content (Table 1).Among the 47 volatiles common to two or three stages, only six volatiles were significantly different in relative contents. Of which, D-limonene was higher at PREO than at OVIP (One-way ANOVA: F = 11.936, df = 2, P = 0.012) or POSO (P = 0.012), and 1-butanol was higher at OVIP than at PREO (One-way ANOVA: F = 8.175, df = 2, P = 0.024) or POSO (P = 0.04). Relative contents of the other four volatiles were less than 1% (Table 1).The volatiles from feces of Przewalski’s horse with different freshness states at the OVIP stage of G. pecorum
    Totally, 83 volatiles were detected from fresh feces (Fresh), semi-fresh feces (Semi-fresh), and dry feces (Dry) at the OVIP stage of G. pecorum. Of which, 48, 41 and 28 volatiles were identified in Fresh, Semi-fresh and Dry, and 7 volatiles were common to all three feces with different freshness states. In addition, 14, 3 and 3, were common between Fresh and Semi-fresh, Semi-fresh and Dry, as well as Fresh and Dry, whereas 24, 17, and 15 were unique to Fresh, Semi-fresh, and Dry, respectively (Table 2; Fig. S2). Aromatic hydrocarbons and alkenes, acids and ketones, as well as alcohols and aldehydes were the two main chemical classes of Fresh, Semi-fresh, and Dry in respective. Except esters and ‘others’ which showed no significant difference in the feces, there were significant differences among other seven classes in at least one pairwise comparison of the three freshness states (One-way ANOVA, Independent t-test or Kruskal–Wallis test: P  More

  • in

    Ecological and health risk assessment of trace metals in water collected from Haripur gas blowout area of Bangladesh

    Physiochemical characteristics of water in the blowout regionThe physiochemical properties of water were measured in the laboratory. The analyzed properties are shown in Table 3.Table 3 The analyzed physiochemical properties of water.Full size tableThe average value of pH is 6.529 indicates water of the study area is slightly acidic in nature. The average value of CO2 (6.5) complied with the lowering tendency of pH. The average ORP value 36 also reflecting the sign of acidic water in the study region. According to WHO standards (2011), the value of conductivity within range 0–800, Total dissolved solids less than 500 ppm, alkalinity 120 ppm, and total hardness less than 300 mg/L are allowable for drinking and domestic purpose37. The average value of conductivity 76.7 µs/cm, total dissolved solids 44.2 ppm, alkalinity 109.1 concurred with the dirking water standard by WHO (2011). The average value of TH is 49 ppm points out that the properties of water are soft.Spatial distribution of trace elements derived from water bodies around the blowout areaThe primary purpose of this study is to understand the concentration level of different Trace metals in the area. In this study, Pb, Ni, Cu, Cd, and Zn were examined (Fig. 3). Besides the toxic metal spatial distribution map is constructed using the inverse distance weighting (IWD) method in Arc GIS (version 10.5). The map (Fig. 4) shows common patterns of hotspots near the Syl-1 blowout area for every metal. This scenario indicates that these metals are originated from the same source46.The contiguous area near Syl-4 well also exhibited a similar pattern to Syl-1 for all metals except Cd. A high concentration of Cd was found closed to the Syl-1 area. The elevated concentration of toxic metals like Ni, Pb, and Cd are found in the adjacent areas of blowout points (Fig. 4). Continuous gas escaping from these abandoned wells might stimulate the trace metal accumulation, especially Pb would be more toxic when it will come to a contact with gasoline (Syl-1 and Syl-4)7. The non-essential toxic metals like Ni, Cd, and Pb in water can pose a serious health threat inthesite47. In addition, these toxic elements can contribute to acute or chronic health issues like high blood pressure, kidney failure, headache, abdominal pain, cancer, nerve damage, and so on for the long-term consumption of such water48.Standard value of Pb in water is 0.01 mg/L, Ni is 0.02 mg/L, Cu is 2 mg/L, Cd is 0.003 mg/L in water37. In this analysis, the average value of Pb = 0.04, Cd = 0.05, Ni = 0.16, Cu = 0.03 mg/L, respectively. The TMs like Zn concentration is about zero or below the detection level for water samples in the study location. The values of Pb, Cd and Ni were higher than the standards level indicates that the water should not be used for any purpose49.Figure 3The concentration of trace elements in the study area.Full size imageFigure 4The spatial distribution map of toxic metals in the area.Full size imageCorrelation coefficient (R) matrix of water quality parameter presented in the blowout areaA Correlation matrix represents the relationship among several variables. It is generated based on the correlation coefficient, which ranges from − 1 to 1. The value of correlation coefficient (1, − 1) indicates perfect correlation, (− 0.9 to − 0.7 or 0.9–0.7) shows strong correlation, (0.4–0.6 either positive or negative) represents moderate correlation, (0.1–0.3 or − 0.1 to − 0.3) displays as weak and 0 indicates no relationship between variables50. The mathematical expressions are described in the article by MacMillan et al.51 to evaluate the correlation coefficient (r).The correlation matrix is shown in Table 4. From the Table 4, it is clear that the pH shows a moderate to strong correlation with CO2 (0.63) and alkalinity (0.69). Whereas, it shows a very strong positive correlation with Total Hardness (TH) and Ca2+ (0.88), respectively. The moderately positive correlation reflects with EC (0.41) and trace elements Ni (0.62). The rest of parameters show a negative correlation. The CO2 exhibits a good correlation with EC (0.72), TH and Ca2+ (0.52). Alkalinity states a good correlation with TH and Calcium ions (0.76). EC shows a maximum correlation with TDS (1.00); maximum correlation also found in the case of TH and Ca2+. Turbidity has a positive correlation for all of the parameters except EC and TDS. TDS shows a strong positive correlation with all of the trace elements, in the case of Pb (0.54), Cd (0.88), Ni (0.68) and for Cu the value is 0.64. All trace elements have a strong correlation with each other. Pb represents a good correlation with Cd (0.65), Ni (0.54) and Cd (0.35). Ni has a strong correlation with Cd (0.61), Cu (0.43). Cu also implies a good correlation with Cd (0.58). In the end, it can be mentioned that a strong positive correlation can be detected among all of the trace elements and also for most of the relative parameters. CO2 established the equilibrium state in the water with ions might be lowering the oxidation. The trace metals Cu and Cd were positively correlated with the turbidity. The washed turbid water from the blow out areas might stimulate these trace metals. The inverse association with oxidation and total hardness indicates the less vegetated areas have higher influx rate of soil materials. It implies the result of the correlation matrix indicated that all of the trace elements and also relevant ions presented in the water of blowout area resultant from the same source46.Table 4 Correlation coefficient matrix of water parameters.Full size tableFactor loading of water parametersThe interrelationship within a set of variables or objects is represented by factor analysis. The factors contain all of the basic information about a wider set of variables or observed objects. It shows how the variables are strongly correlated with the determined factor. Factor analysis is also known as a multivariate approach to reducing data33. Among different types of factor analysis, Principal component analysis account for the maximum variance of observed variables. So, it can be called variance-oriented33. Factor loading shows how certain variables strongly correlate for a given factor. Factor loading varies from − 1 to + 1 where the value of factor loading below − 0.5 or above 0.5 suggested good correlations and value closed to − 1 or + 1, suggesting a more robust correlation32. The Table 5 represented the principal component analysis result of factor solution.Table 5 Principal components analysis results of water parameters.Full size tableFrom analysis (Table 5), it can be realized that the water quality parameters such as Turbidity, TH, Ca2+, Cd, Ni and Cu have a stronger correlation with each other’s reflecting their source of origin might be from the same area14. Factor loading also suggested that more robust interconnection exists among CO2, EC and TDS. In this analysis, the two-factor solution explained approximately 80.6% of the variance. The eigenvalue, total variance explained are represented in Supplementary Table S1. That percentage is high enough to accept the results. It can also be added that the red and yellow colored loading represented strong correlation with each other46,52.Water quality index (WQI)The WQI is one of the best tools for monitoring the surface-groundwater contamination and can be used for water quality improvement programs. The WQI is determined from various  physicochemical parameters like pH, EC, TDS, TH, EC, and so forth. Higher estimation of WQI indicates poor water quality and lower estimation of WQI shows better water quality. During this examination, WQI esteems a range from 0.02633 to 5144.37 and are characterized into five water types shown in Table 6. The noteworthy WQI is recorded in case of (sample-1) which demonstrates an elevated level of contamination. Water sample 2, 5, 8 and 10 are grouped under class-1 which demonstrates there is a lower degree of pollution in water. In addition, WQI calculation for sample 2, 5, 8 and 10 excluded trace elements value and WQI evaluation for sample 1, 3, 4, 6, 7 and 9 included the heavy metals value in water. These results also clarify the association of heavy metals on water quality degradation of the study area.Table 6 Classification of the water quality index for individual parameter of water.Full size tableThe situation of contamination in the areaThe level of contamination has been demonstrated in terms of the CFi, PLI, and also PI analysis of water samples around the blowout area. The values of CFi are indicated the degree of contamination. The intensity of CFi has been determined with some numerical values like 1, 3, and 6. The CFi value is less than 1, which implies low contamination, as the value is > 6 indicated a high degree of contamination36. The Table 7 elucidates that the degree of contamination in the case of trace elements Pb, Cd, and Ni are very high for most of the locations of the research sides. Besides Cu and Zn exhibit that level contamination is low in the area. In other cases, the PLI can be evaluated by using the CFi value. The value of PLI greater than 1 symbolizes polluted and less than 1 represents the unpolluted status36,39. The pollution load index rate of Pb, Cd, and Ni are 2.3, 2.87, and 2.56, respectively (Fig. 5).This result indicates the pollution of water bodies in the sampling sites. The other elements such as Cu and Zn are within the allowable limit are shown in Fig. 5. Moreover, the PI indicates similar results as CFi and PLI.Table 7 Contamination factor of water samples.Full size tableFigure 5Pollution load index of the study area.Full size imageThe state of potential ecological threat in the areaThe ecological potential risk index has been appealed to detect the possible threat to the ecological system in the adjoining area. The calculated RI value provided the risk factor of water for understanding the ecological threat. When the RI value is more than 600, it is considered a polluted case11,14,36. The computed RI value of the study for Pb, Cd, Ni, and Cu are 123.5, 2770, 235, and 0.23, respectively (Table 8). The value of Cd is high enough (RI  > 600). So, the Cd values indicated that the potential threat to the ecological system. Besides, the TMs like Ni and Cu are specified medium to low ecological pollution in the area are shown in Table 8. Moreover, the spatial distribution has been presented to outlook the potential ecological threats around the blow out location of the gas field is shown in Fig. 6.Table 8 Ecological risk index (RI) of the study area.Full size tableFigure 6A map of the spatial distribution of potential ecological risk threats in the study area.Full size imageThe spatial distribution map of RI also pointed out the high ecological risk closed to the blowout areas (Fig. 6). From these results, it can be implied that the use of  this water for domestic or drinking purposes, can be harmful for living beings. Moreover, it can be distressed the ecological system in the site. Hence, the use of the water from this site should be avoided by dwellers near the blowout areas of the gas field.Assessment of noncarcinogenic health risksNoncarcinogenic risk is one of the vital categories of human health risk assessment. It is known that a polluted environment is highly liable for causing a health risk. Toxic metal presents in water also very harmful for public health, including child and adult both. The health risks may be extended through ingestion and skin absorption of water. To know the harmful impacts of trace elements of water on the human body, noncarcinogenic risk evaluation is more important. For that, the value of CDI for ingestion and dermal absorption was evaluated at the beginning to identify such risk index (Supplementary Table S2 and S3). Then the CDI has been divided with the RfD value. From where, the HQ can be acquired separately for ingestion and dermal absorption. The summation of HQingestion and HQdermal expressed the HQtotal. And the HQtotal entirety was used to achieve the HI are shown in Table 9.Table 9 The HQ and hazard index (HI) value of noncarcinogenic analysis of the area.Full size tableThe results elucidate that case of adult, the mean value of CDITotal for Pb is 1.29E-03, Cd is 1.45E-03, Ni is 4.93E-03 and Cu is 4.83E-04, respectively. For the child, the mean value of CDITotal in the case of Pb, Cd, Ni, and CU is4.7544E-03, 5.33E-03, 1.81E-03 and 1.77E-04, correspondingly. Additionally, the order of CDITotal for adults are Ni  > Cd  > Pb  > Cu (Supplementary Table S2) whereas, for child, it is quite different. In the case of children, the order  are Cd  > Pb  > Ni  > Cu are presented in Supplementary Table S3.The mean values of HQTotal of Pb, Cd, Cu, and Ni are ranging from 4.46E−05 to 1.45E−02 for child. Besides, these values for adults are extending from 1.21E−05 to 4.66E−03. These values suggest that the trace elements in the water of the study area are quite harmful to the child than an adult. The children’s HQTotal has been ordered as Cd  > Pb  > Ni  > Cu and for the adult Cu  More

  • in

    Influences of conservation measures on runoff and sediment yield in different intra-event-based flood regimes in the Chabagou watershed

    Effects on intra-event-based flood runoff and sediment characteristicsBetween the 1960s and 1990s, there was no significant change in rainfall in the Chabagou watershed35. The mean values of runoff and sediment transport in the baseline period and measurement period were calculated. Regardless of rainfall influence, the effect of conservation measures was assessed by the time series contrasting method25.Table 1 shows the statistics of the characteristics of event-based flood flows and sediment in 1961–1990 (excluding 1970). Compared with those in the baseline period, T and Tr in the measurement period increased by 16.54% and 29.21%, respectively; however, Tp decreased by 55.52% in the measurement period, which showed that the soil and water conservation measures extended the flood duration while reducing the time of increased discharge. Under identical rainfall conditions, long-duration runoff with less time for increased discharge could cause less erosion than short-duration runoff with more time for increased discharge36. Hence, the conservation measures reduced soil erosion by prolonging the flood duration and reducing the time to peak. In addition, the hydrodynamic indices qp, H and qm were 75.2%, 56.0% and 68.0% lower, respectively, in the measurement period than in the baseline period. Moreover, E in the measurement period was only 10.2% that in the baseline period. The results showed that the conservation measures greatly reduced the hydrodynamic energy and thus soil erosion. In addition, the relative erosion indicators SSY, SCE and MSCE, decreased 69.2%, 33.3%, and 11.9%, respectively, in the measurement period compared with the baseline period, which indicated that the conservation measures significantly reduced soil erosion and decreased the mean sediment concentration, although the reduction in the maximum sediment concentration was relatively small. The conservation measures, especially the engineering measures, reduced the runoff velocity, extended the flood duration, and reduced the peak discharge, which sharply reduced the runoff erosion power37,38. As a consequence of the decrease in erosive energy, soil erosion was diminished.Table 1 Descriptive statistics of the characteristics of event-based flood flows and sediment in 1961–1990 (excluding 1970).Full size tableInfluence on intra-event-based flood regimesClassification of flood events and the characteristics of baseline period flood regimesFigure 2 shows the clustering results of the flood events at the Caoping hydrological station in 1961–1969. The flood events were divided into 4 regimes with a significance level of p  More

  • in

    MFCIS: an automatic leaf-based identification pipeline for plant cultivars using deep learning and persistent homology

    1.Sohn, H. B. et al. Barcode system for genetic identification of soybean [Glycine max (L.) Merrill] cultivars using InDel markers specific to dense variation blocks. Front. Plant Sci. 8, 520 (2017).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    2.Korir, N. K. et al. Plant variety and cultivar identification: advances and prospects. Crit. Rev. Biotechnol. 33, 111–125 (2013).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    3.Jamali, S. et al. Identification and distinction of soybean commercial cultivars using morphological and microsatellite markers., Iranian. J. Crop Sci. 13, 131–145 (2011).
    Google Scholar 
    4.Wu, K. et al. Genetic analysis and molecular characterization of Chinese sesame (Sesamum indicum L.) cultivars using Insertion-Deletion (InDel) and Simple Sequence Repeat (SSR) markers. BMC Genet. 15, 35 (2014).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    5.Lee, S. H. et al. How deep learning extracts and learns leaf features for plant classification. Pattern Recognit. 71, 1–13 (2017).Article 

    Google Scholar 
    6.Zhao, C., Chan, S. S. F., Cham, W.-K. & Chu, L. M. Plant identification using leaf shapes: a pattern counting approach. Pattern Recognit. 48, 3203–3215 (2015).Article 

    Google Scholar 
    7.Price, C. A. et al. Leaf extraction and analysis framework graphical user interface: segmenting and analyzing the structure of leaf veins and areoles. Plant Physiol. 155, 236–245 (2011).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    8.De Vylder, J., Vandenbussche, F. & Hu, Y. et al. Rosette tracker: an open source image analysis tool for automatic quantification of genotype effects[J]. Plant physiology 160, 1149–1159 (2012).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    9.Zhou, J. et al. Leaf-GP: an open and automated software application for measuring growth phenotypes for arabidopsis and wheat. Plant Methods 13, 117 (2017).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    10.Biot, E. et al. Multi-scale quantification of morphodynamics: MorphoLeaf software for 2D shape analysis. Development 143, 3417–3428 (2016).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    11.Minervini, M. et al. Phenotiki: an open software and hardware platform for affordable and easy image-based phenotyping of rosette-shaped plants. Plant J. 90, 204–216 (2017).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    12.Neto, J. C. et al. Plant species identification using Elliptic Fourier leaf shape analysis. Computers Electron. Agriculture 50, 121–134 (2006).Article 

    Google Scholar 
    13.Cope, J. S. et al. in International Symposium on Visual Computing (eds Bebis, G. et al.) 669–677 (Springer, 2010).14.Chaki, J. & Parekh, R. Plant leaf recognition using shape based features and neural network classifiers, Int. J. Adv. Comp. Sci. Appl. 2, 41–47 (2011).15.Naresh, Y. & Nagendraswamy, H. Classification of medicinal plants: an approach using modified LBP with symbolic representation. Neurocomputing 173, 1789–1797 (2016).Article 

    Google Scholar 
    16.Pradeep Kumar, T., Veera Prasad Reddy, M. & Bora, P. K. Leaf identification using shape and texture features. Proceedings of International Conference on Computer Vision and Image Processing (eds Raman B., Kumar S., Roy P. P., Sen D.) 531–541 (Springer Singapore, 2017).17.Tharwat, A., Gaber, T., Awad, Y. M., Dey, N. & Hassanien, A. E. Plants identification using feature fusion technique and bagging classifier. (eds Gaber T., Hassanien A. E., El-Bendary N., Dey N.). The 1st International Conference on Advanced Intelligent System and Informatics (AISI2015), November 28–30, 2015, Beni Suef, Egypt. 461–471 (Springer International Publishing, 2016).18.Codizar, A. L. & Solano, G. Plant leaf recognition by venation and shape using artificial neural networks. In: 2016 7th International Conference on Information,Intelligence, Systems & Applications (IISA). 1–4 (IEEE, 2016).19.Yang, C. Plant leaf recognition by integrating shape and texture features. Pattern Recognit. 112, 107809 (2021).Article 

    Google Scholar 
    20.Liu, C. et al. A novel identification method for apple (Malus domestica Borkh.) cultivars based on a deep convolutional neural network with leaf image input. Symmetry 12, 217 (2020).Article 

    Google Scholar 
    21.Baldi, A. et al. A leaf-based back propagation neural network for oleander (Nerium oleander L.) cultivar identification. Computers Electron. Agriculture 142, 515–520 (2017).Article 

    Google Scholar 
    22.X. Yu, et al. Patchy image structure classification using multi-orientation region transform. in Proceedings of the AAAI Conference on Artificial Intelligence. 12741–12748 (AAAI, 2020).23.Edelsbrunner, H & Harer, J. in Persistent Homology—a Survey (eds Goodman, J. E., Pach, J., Pollack, R.). 257–282 (Contemporary Mathematics American Mathematical Society, 2008).24.Li, M. et al. Topological data analysis as a morphometric method: using persistent homology to demarcate a leaf morphospace. Front. Plant Sci. 9, 553 (2018).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    25.Reininghaus, J. et al. A stable multi-scale kernel for topological machine learning, in: 2015 IEEE Conference on Computer Vision and Pattern Recognition (CVPR) 4741–4748 (IEEE, Boston, MA, USA, 2015).26.Li, C., Ovsjanikov, M. & Chazal, F. Persistence-based structural recognition. in Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition. 1995–2002 (IEEE Computer Society, 2014).27.Dey, T., Mandal, S. & Varcho, W. Improved image classification using topological persistence. in Proceedings of the Conference on Vision, Modeling and Visualization. 161–168 (Eurographics Association, 2017).28.MacLane, S. Homology. Bull. Am. Math. Soc. 70, 329–331 (1964).Article 

    Google Scholar 
    29.Qaiser, T. et al. Tumor segmentation in whole slide images using persistent homology and deep convolutional features. in Annual Conference on Medical Image Understanding and Analysis. 320–329 (Springer, 2017).30.Qaiser, T. et al. Fast and accurate tumor segmentation of histology images using persistent homology and deep convolutional features. Med. Image Anal. 55, 1–14 (2019).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    31.Zeppelzauer, M. et al. A study on topological descriptors for the analysis of 3d surface texture. Computer Vis. Image Underst. 167, 74–88 (2018).Article 

    Google Scholar 
    32.Chollet, F. Xception: Deep learning with depthwise separable convolutions. in Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition. 1251–1258 (IEEE Computer Society, 2017).33.Hofer, C. et al. Deep learning with topological signatures. In: Advances in Neural Information Processing Systems. 1634–1644 (Curran Associates Inc., 2017).34.Turner, K., Mukherjee, S. & Boyer, D. M. Persistent homology transform for modeling shapes and surfaces. Inf. Inference.: A J. IMA 3, 310–344 (2014).Article 

    Google Scholar 
    35.Deng, J. et al. Imagenet: a large-scale hierarchical image database. in 2009 IEEE Conference on Computer Vision and Pattern Recognition. 248–255 (IEEE, 2009).36.Adams, H. et al. Persistence images: A stable vector representation of persistent homology. J. Mach. Learn. Res. 18, 218–252 (2017).
    Google Scholar 
    37.Bubenik, P. Statistical topological data analysis using persistence landscapes. J. Mach. Learn. Res. 16, 77–102 (2015).
    Google Scholar 
    38.Wang, B. et al. From species to cultivar: Soybean cultivar recognition using joint leaf image patterns by multi-scale sliding chord matching. Biosyst. Eng. 194, 99–111 (2020).Article 

    Google Scholar 
    39.Heiberger, R. M., & Neuwirth E. One-way ANOVA. In: R through Excel. 165–191 (Springer, 2009).40.Ling, H. & Jacobs, D. W. Shape classification using the inner-distance. IEEE Trans. Pattern Anal. Mach. Intell. 29, 286–299 (2007).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    41.Wang, B. & Gao, Y. Hierarchical string cuts: a translation, rotation, scale, and mirror invariant descriptor for fast shape retrieval. IEEE Trans. Image Process 23, 4101–4111 (2014).42.Kaya, A. et al. Analysis of transfer learning for deep neural network-based plant classification models. Computers Electron. Agriculture 158, 20–29 (2019).Article 

    Google Scholar 
    43.Yanping, Z. & Liu, W. WeizhenLiuBioinform/mfcis: source code of mfcis. (Version 1.0.2). Zenodo https://doi.org/10.5281/zenodo.4739746 (2021).44.Barré, P. et al. LeafNet: a computer vision system for automatic plant species identification. Ecol. Inform. 40, 50–56 (2017).Article 

    Google Scholar 
    45.Beghin, T. et al. Shape and texture-based plant leaf classification. in International Conference on Advanced Concepts for Intelligent Vision Systems, 345–353 (Springer, 2010).46.Blonder, B. et al. X-ray imaging of leaf venation networks. N. Phytologist 196, 1274–1282 (2012).Article 

    Google Scholar 
    47.Gan, Y. et al. Automatic hierarchy classification in venation networks using directional morphological filtering for hierarchical structure traits extraction. Computational Biol. Chem. 80, 187–194 (2019).CAS 
    Article 

    Google Scholar 
    48.Cui, F. & Yang, G. Score level fusion of fingerprint and finger vein recognition. J. Computational Inf. Syst. 7, 5723–5731 (2011).
    Google Scholar 
    49.Park, H.-A. & Park, K. R. Iris recognition based on score level fusion by using SVM. Pattern Recognit. Lett. 28, 2019–2028 (2007).Article 

    Google Scholar 
    50.Ghosh, S. et al. Software for systems biology: from tools to integrated platforms. Nat. Rev. Genet. 12, 821–832 (2011).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    51.Smulders, M., Booy, I. & Vosman, B. Use of molecular and biochemical methods for identification of plant varieties throughout the agri-chain. (eds Trienekens, J. H. & Zuurbier, P. J. P.) In Proceedings of the 2nd International Conference on Chain Management in Agri-and Food Business. 591–600 (Department of Management studies Wageningen Agricultural University, May 1996).52.Park, H. et al. Molecular identification of sweet potato accessions using ARMS-PCR based on SNPs. J. Plant Biotechnol. 47, 124–130 (2020).Article 

    Google Scholar 
    53.Fufa, H. et al. Comparison of phenotypic and molecular marker-based classifications of hard red winter wheat cultivars. Euphytica 145, 133–146 (2005).CAS 
    Article 

    Google Scholar 
    54.Kim, M. et al. Genome-wide SNP discovery and core marker sets for DNA barcoding and variety identification in commercial tomato cultivars. Sci. Horticulturae 276, 109734 (2021).CAS 
    Article 

    Google Scholar 
    55.Patzak, J., Henychová, A., Paprštein, F. & Sedlák, J. Evaluation of S-incompatibility locus, genetic diversity and structure of sweet cherry (Prunus avium L.) genetic resources by molecular methods and phenotypic characteristics. J. Horticultural Sci. Biotechnol. 95, 84–92 (2020).CAS 
    Article 

    Google Scholar 
    56.Pourkhaloee, A. et al. Molecular analysis of genetic diversity, population structure, and phylogeny of wild and cultivated tulips (Tulipa L.) by genic microsatellites. Horticulture Environ. Biotechnol. 59, 875–888 (2018).CAS 
    Article 

    Google Scholar 
    57.Cho, K. H. et al. Sequence-characterized amplified region markers and multiplex-polymerase chain reaction assays for kiwifruit cultivar identification. Horticulture Environ., Biotechnol. 61, 395–406 (2020).CAS 
    Article 

    Google Scholar 
    58.Agarwal, M., Shrivastava, N. & Padh, H. Advances in molecular marker techniques and their applications in plant sciences. Plant Cell Rep. 27, 617–631 (2008).CAS 
    PubMed 
    Article 

    Google Scholar 
    59.Nadeem, M. A. et al. DNA molecular markers in plant breeding: current status and recent advancements in genomic selection and genome editing. Biotechnol. Biotechnological Equip. 32, 261–285 (2018).CAS 
    Article 

    Google Scholar 
    60.Yamaç, S. S. & Todorovic, M. Estimation of daily potato crop evapotranspiration using three different machine learning algorithms and four scenarios of available meteorological data. Agric. Water Manag. 228, 105875 (2020).Article 

    Google Scholar 
    61.Reisi Gahrouei, O., McNairn, H., Hosseini, M. & Homayouni, S. Estimation of crop biomass and leaf area index from multitemporal and multispectral imagery using machine learning approaches. Can. J. Remote Sens. 46, 84–99 (2020).Article 

    Google Scholar 
    62.Colmer, J. et al. SeedGerm: a cost-effective phenotyping platform for automated seed imaging and machine-learning based phenotypic analysis of crop seed germination. N. Phytologist 228, 778–793 (2020).CAS 
    Article 

    Google Scholar 
    63.Danner, M., Berger, K., Wocher, M., Mauser, W. & Hank, T. Efficient RTM-based training of machine learning regression algorithms to quantify biophysical & biochemical traits of agricultural crops. ISPRS J. Photogramm. Remote Sens. 173, 278–296 (2021).Article 

    Google Scholar 
    64.Zeiler, M. D. & Fergus R. in Visualizing and Understanding Convolutional Networks (eds Fleet D., Pajdla T., Schiele B., Tuytelaars T.). Computer Vision–ECCV 2014. 818–833 (Springer International Publishing, 2014).65.Erhan, D., Bengio, Y., Courville, A. & Vincent, P. Visualizing higher-layer features of a deep network. Univ. Montr. 1341, 1 (2009).
    Google Scholar 
    66.Simonyan, K., Vedaldi, A. & Zisserman, A. Deep inside convolutional networks: Visualising image classification models and saliency maps[C]//InWorkshop at International Conference on Learning Representations. (2014).67.Islam, M. R. Feature and score fusion based multiple classifier selection for iris recognition. Computational Intell. Neurosci. 2014, e380585 (2014).Article 

    Google Scholar 
    68.Yang, J. et al. Feature fusion: parallel strategy vs. serial strategy. Pattern Recognit. 36, 1369–1381 (2003).Article 

    Google Scholar 
    69.Bryson, A. E. et al. Composite modeling of leaf shape across shoots discriminates Vitis species better than individual leaves. Preprint at bioRxiv https://doi.org/10.1101/2020.06.22.163899 (2020). More

  • in

    Integrating plant-to-plant communication and rhizosphere microbial dynamics: ecological and evolutionary implications and a call for experimental rigor

    1.Heil M, Karban R. Explaining evolution of plant communication by airborne signals. Trends Ecol Evol. 2010;25:137–44.Article 

    Google Scholar 
    2.Rubin IN, Ellner SP, Kessler A, Morrell KA. Informed herbivore movement and interplant communication determine the effects of induced resistance in an individual-based model. J Anim Ecol. 2015;84:1273–85.Article 

    Google Scholar 
    3.Kalske A, Shiojiri K, Uesugi A, Sakata Y, Morrell K, Kessler A. Insect herbivory selects for volatile-mediated plant-plant communication. Curr Biol. 2019;29:3128–33.CAS 
    Article 

    Google Scholar 
    4.Frisen ML, Porter SS, Stark SC, von Wettberg EJ, Sachs JL, Martinez-Romero E. Microbially mediated plant functional traits. Ann Rev Ecol Evol Syst. 2011;42:23–46.Article 

    Google Scholar 
    5.Lebeis SL, Herrera Paredes S, Lundberg DS, Breakfield N, Gehrin J, McDonald M, et al. Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa. Science. 2015;349:860–4.CAS 
    Article 

    Google Scholar 
    6.Berendsen RL, Vismans G, Yu K, Song Y, de Jonge R, Burgman WP, et al. Disease-induced assemblage of a plant-beneficial bacterial consortium. ISME J. 2018;12:1496–507.CAS 
    Article 

    Google Scholar 
    7.Pieterse CMJ, Zamioudis C, Berendsen RL, Weller DM, Van Wees SCM, Bakker PAHM. Induced systemic resistance by beneficial microbes. Ann Rev Phytopathol. 2014;52:347–75.CAS 
    Article 

    Google Scholar 
    8.Frank L, Wenig M, Ghirardo A, van der Krol A, Vlot AC, Schnitzler J-P, et al. Isoprene and β-caryophyllene confer plant resistance via different plant internal signaling pathways. Plant Cell Environ. 2021;44:1151–64.CAS 
    Article 

    Google Scholar 
    9.Kong HG, Song GC, Sim H-J, Ryu C-M. Achieving similar root microbiota composition in neighbouring plants through airborne signalling. ISME J. 2021;15:397–408.CAS 
    Article 

    Google Scholar 
    10.Dicke M, Bruin J. Chemical information transfer between plants: back to the future. Biochem Syst Ecol. 2001;29:981–94.CAS 
    Article 

    Google Scholar 
    11.Peacher MD, Meiners SJ. Inoculum handling alters the strength and direction of plant-microbe interactions. Ecology. 2020;4:e02994.
    Google Scholar 
    12.Pieterse CMJ, Van der Does D, Zamioudis C, Leon-Reyes A, Van Wees SCM. Hormonal modulation of plant immunity. Ann Rev Cell Dev Biol. 2012;28:489–521.CAS 
    Article 

    Google Scholar 
    13.Erb M. Volatiles as inducers and suppressors of plant defense and immunity—origins, specificity, perception, and signalling. Curr Opin Plant Biol. 2018;44:117–21.CAS 
    Article 

    Google Scholar 
    14.Nagashima A, Higaki T, Koeduka T, Ishigami K, Hosokawa S, Watanabe H, et al. Transcriptional regulators involved in responses to volatile organic compounds in plants. J Biol Chem. 2019;294:2256–66.CAS 
    Article 

    Google Scholar 
    15.Khorassani R, Hettwer U, Ratzinger A, Steingrobe B, Karlovsky P, Claassen N. Citramalic acid and salicylic acid in sugar beet root exudates solubilize soil phosphorus. BMC Plant Biol. 2011;11:21.Article 

    Google Scholar 
    16.Fitzpatrick CR, Copeland J, Wang PW, Guttman DS, Kotanen PM, Johnson MTJ. Assembly and ecological function of the root microbiome across angiosperm plant species. Proc Natl Acad Sci. 2018;115:E1157–65.CAS 
    Article 

    Google Scholar 
    17.Crawford KM, Bauer JT, Comita LS, Eppinga MB, Johnson DJ, Mangan SA, et al. When and where plant-soil feedback may promote plant coexistence: a meta-analysis. Ecol Lett. 2019;22:1274–84.Article 

    Google Scholar 
    18.Tidbury HJ, Best A, Boots M. The epidemiological consequences of immune priming. Proc R Soc B: Biol Sci. 2015;279:4505–12.Article 

    Google Scholar 
    19.Wagner MR, Lundberg DS, Coleman-Derr D, Tringe SG, Dangl JL, Mitchell-Olds T. Natural soil microbiomes alter flowering phenology and the intensity of selection of flowering time in a wild Arabidopsis relative. Ecol Lett. 2014;17:717–26.Article 

    Google Scholar 
    20.Petipas RH, Geber MA, Lau JA. Microbe-mediated adaptation in plants. Ecol Lett. 2021;24:1302–17. More

  • in

    Lytic archaeal viruses infect abundant primary producers in Earth’s crust

    1.Flemming, H. C. & Wuertz, S. Bacteria and archaea on Earth and their abundance in biofilms. Nat. Rev. Microbiol. 17, 247–260 (2019).CAS 
    PubMed 
    Article 

    Google Scholar 
    2.Magnabosco, C. et al. The biomass and biodiversity of the continental subsurface. Nat. Geosci. 11, 707–717 (2018).CAS 
    Article 
    ADS 

    Google Scholar 
    3.Anantharaman, K. et al. Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system. Nat. Commun. 7, 13219 (2016).CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar 
    4.Hug, L. A. et al. A new view of the tree of life. Nat. Microbiol. 1, 16048 (2016).CAS 
    PubMed 
    Article 

    Google Scholar 
    5.Castelle, C. J. et al. Genomic expansion of domain archaea highlights roles for organisms from new phyla in anaerobic carbon cycling. Curr. Biol. 25, 690–701 (2015).CAS 
    PubMed 
    Article 

    Google Scholar 
    6.Nunoura, T. et al. Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group. Nucleic Acids Res. 39, 3204–3223 (2011).CAS 
    PubMed 
    Article 

    Google Scholar 
    7.Probst, A. J. et al. Biology of a widespread uncultivated archaeon that contributes to carbon fixation in the subsurface. Nat. Commun. 5, 5497 (2014).CAS 
    PubMed 
    Article 
    ADS 

    Google Scholar 
    8.Zaremba-Niedzwiedzka, K. et al. Asgard archaea illuminate the origin of eukaryotic cellular complexity. Nature 541, 353–358 (2017).CAS 
    PubMed 
    Article 
    ADS 

    Google Scholar 
    9.Weinbauer, M. G. & Rassoulzadegan, F. Are viruses driving microbial diversification and diversity? Environ. Microbiol. 6, 1–11 (2004).PubMed 
    Article 

    Google Scholar 
    10.Engelhardt, T., Kallmeyer, J., Cypionka, H. & Engelen, B. High virus-to-cell ratios indicate ongoing production of viruses in deep subsurface sediments. ISME J. 8, 1503–1509 (2014).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    11.Danovaro, R. et al. Virus-mediated archaeal hecatomb in the deep seafloor. Sci. Adv. 2, e1600492 (2016).PubMed 
    PubMed Central 
    Article 
    ADS 
    CAS 

    Google Scholar 
    12.Kyle, J. E., Eydal, H. S., Ferris, F. G. & Pedersen, K. Viruses in granitic groundwater from 69 to 450 m depth of the Äspö hard rock laboratory, Sweden. ISME J. 2, 571–574 (2008).PubMed 
    Article 

    Google Scholar 
    13.Labonté, J. M. et al. Single cell genomics indicates horizontal gene transfer and viral infections in a deep subsurface Firmicutes population. Front. Microbiol. 6, 349 (2015).PubMed 
    PubMed Central 

    Google Scholar 
    14.Hylling, O. et al. Two novel bacteriophage genera from a groundwater reservoir highlight subsurface environments as underexplored biotopes in bacteriophage ecology. Sci. Rep. 10, 11879 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar 
    15.Daly, R. A. et al. Viruses control dominant bacteria colonizing the terrestrial deep biosphere after hydraulic fracturing. Nat. Microbiol. 4, 352–361 (2019).CAS 
    PubMed 
    Article 

    Google Scholar 
    16.Horvath, P. & Barrangou, R. CRISPR/Cas, the immune system of bacteria and archaea. Science 327, 167–170 (2010).CAS 
    PubMed 
    Article 
    ADS 

    Google Scholar 
    17.Pauly, M. D., Bautista, M. A., Black, J. A. & Whitaker, R. J. Diversified local CRISPR-Cas immunity to viruses of Sulfolobus islandicus. Philos. Trans. R. Soc. Lond. B Biol. Sci. 374, 20180093 (2019).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    18.Probst, A. J. et al. Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface. Nat. Microbiol. 3, 328–336 (2018).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    19.Henneberger, R., Moissl, C., Amann, T., Rudolph, C. & Huber, R. New insights into the lifestyle of the cold-loving SM1 euryarchaeon: natural growth as a monospecies biofilm in the subsurface. Appl. Environ. Microbiol. 72, 192–199 (2006).CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar 
    20.Probst, A. J. et al. Tackling the minority: sulfate-reducing bacteria in an archaea-dominated subsurface biofilm. ISME J. 7, 635–651 (2013).CAS 
    PubMed 
    Article 

    Google Scholar 
    21.Bird, J. T., Baker, B. J., Probst, A. J., Podar, M. & Lloyd, K. G. Culture independent genomic comparisons reveal environmental adaptations for Altiarchaeales. Front. Microbiol. 7, 1221 (2016).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    22.Hernsdorf, A. W. et al. Potential for microbial H2 and metal transformations associated with novel bacteria and archaea in deep terrestrial subsurface sediments. ISME J. 11, 1915–1929 (2017).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    23.Moissl, C., Rachel, R., Briegel, A., Engelhardt, H. & Huber, R. The unique structure of archaeal ‘hami’, highly complex cell appendages with nano-grappling hooks. Mol. Microbiol. 56, 361–370 (2005).CAS 
    PubMed 
    Article 

    Google Scholar 
    24.Rudolph, C., Wanner, G. & Huber, R. Natural communities of novel archaea and bacteria growing in cold sulfurous springs with a string-of-pearls-like morphology. Appl. Environ. Microbiol. 67, 2336–2344 (2001).CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar 
    25.Rudolph, C., Moissl, C., Henneberger, R. & Huber, R. Ecology and microbial structures of archaeal/bacterial strings-of-pearls communities and archaeal relatives thriving in cold sulfidic springs. FEMS Microbiol. Ecol. 50, 1–11 (2004).CAS 
    PubMed 
    Article 

    Google Scholar 
    26.Schwank, K. et al. An archaeal symbiont-host association from the deep terrestrial subsurface. ISME J. 13, 2135–2139 (2019).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    27.Probst, A. J. & Moissl-Eichinger, C. “Altiarchaeales”: uncultivated archaea from the subsurface. Life 5, 1381–1395 (2015).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    28.Makarova, K. S. et al. Dark matter in archaeal genomes: a rich source of novel mobile elements, defense systems and secretory complexes. Extremophiles 18, 877–893 (2014).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    29.Vik, D. R. et al. Putative archaeal viruses from the mesopelagic ocean. PeerJ 5, e3428 (2017).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    30.Anderson, R. E., Brazelton, W. J. & Baross, J. A. The deep viriosphere: assessing the viral impact on microbial community dynamics in the deep subsurface. Carbon Earth 75, 649–675 (2013).CAS 
    Article 

    Google Scholar 
    31.Rodrigues, R. A. L. et al. An anthropocentric view of the virosphere-host relationship. Front. Microbiol. 8, 1673 (2017).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    32.Munson-McGee, J. H., Snyder, J. C. & Young, M. J. Archaeal viruses from high-temperature environments. Genes 9, 128 (2018).PubMed Central 
    Article 
    CAS 
    PubMed 

    Google Scholar 
    33.Paez-Espino, D. et al. Uncovering Earth’s virome. Nature 536, 425–430 (2016).CAS 
    PubMed 
    Article 
    ADS 

    Google Scholar 
    34.Philosof, A. et al. Novel abundant oceanic viruses of uncultured marine group II Euryarchaeota. Curr. Biol. 27, 1362–1368 (2017).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    35.Ahlgren, N. A., Fuchsman, C. A., Rocap, G. & Fuhrman, J. A. Discovery of several novel, widespread, and ecologically distinct marine Thaumarchaeota viruses that encode amoC nitrification genes. ISME J. 13, 618–631 (2019).CAS 
    PubMed 
    Article 

    Google Scholar 
    36.Gudbergsdottir, S. R., Menzel, P., Krogh, A., Young, M. & Peng, X. Novel viral genomes identified from six metagenomes reveal wide distribution of archaeal viruses and high viral diversity in terrestrial hot springs. Environ. Microbiol. 18, 863–874 (2016).CAS 
    PubMed 
    Article 

    Google Scholar 
    37.Munson-McGee, J. H., Rooney, C. & Young, M. J. An uncultivated virus infecting a nanoarchaeal parasite in the hot springs of Yellowstone National Park. J. Virol. 94, e01213-19 (2020).38.Zablocki, O., van Zyl, L. J., Kirby, B. & Trindade, M. Diversity of dsDNA viruses in a South African hot spring assessed by metagenomics and microscopy. Viruses 9, 348 (2017).PubMed Central 
    Article 
    CAS 
    PubMed 

    Google Scholar 
    39.Emerson, J. B. et al. Host-linked soil viral ecology along a permafrost thaw gradient. Nat. Microbiol. 3, 870–880 (2018).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    40.Trubl, G. et al. Soil viruses are underexplored players in ecosystem carbon processing. mSystems 3, 338103 (2018).Article 

    Google Scholar 
    41.Hochstein, R. A., Amenabar, M. J., Munson-McGee, J. H., Boyd, E. S. & Young, M. J. Acidianus tailed spindle virus: a new archaeal large tailed spindle virus discovered by culture-independent methods. J. Virol. 90, 3458–3468 (2016).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    42.Jahn, M. T. et al. Lifestyle of sponge symbiont phages by host prediction and correlative microscopy. ISME J. 15, 1–11 (2021).43.Anderson, R. E., Brazelton, W. J. & Baross, J. A. Is the genetic landscape of the deep subsurface biosphere affected by viruses? Front. Microbiol. 2, 219 (2011).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    44.Chen, I. A. et al. IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes. Nucleic Acids Res. 47, D666–D677 (2019).CAS 
    PubMed 
    Article 

    Google Scholar 
    45.Bornemann, T. L. V. et al. Geological degassing enhances microbial metabolism in the continental subsurface. https://doi.org/10.1101/2020.03.07.980714 (2020).46.Sharrar, A. M. et al. Novel large sulfur bacteria in the metagenomes of groundwater-fed chemosynthetic microbial mats in the Lake Huron Basin. Front. Microbiol. 8, 791 (2017).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    47.Roux, S., Enault, F., Hurwitz, B. L. & Sullivan, M. B. VirSorter: mining viral signal from microbial genomic data. PeerJ 3, e985 (2015).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    48.Kieft, K. et al. Virus-associated organosulfur metabolism in human and environmental systems. Cell Reports, in press (2021).49.Allers, E. et al. Single-cell and population level viral infection dynamics revealed by phageFISH, a method to visualize intracellular and free viruses. Environ. Microbiol. 15, 2306–2318 (2013).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    50.Roux, S. et al. Minimum information about an uncultivated virus genome (MIUViG). Nat. Biotechnol. 37, 29–37 (2019).CAS 
    PubMed 
    Article 

    Google Scholar 
    51.Breitbart, M. & Rohwer, F. Here a virus, there a virus, everywhere the same virus? Trends Microbiol. 13, 278–284 (2005).CAS 
    PubMed 
    Article 

    Google Scholar 
    52.Short, C. M. & Suttle, C. A. Nearly identical bacteriophage structural gene sequences are widely distributed in both marine and freshwater environments. Appl. Environ. Microbiol. 71, 480–486 (2005).CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar 
    53.Bautista, M. A., Black, J. A., Youngblut, N. D. & Whitaker, R. J. Differentiation and structure in Sulfolobus islandicus rod-shaped virus populations. Viruses 9, 120 (2017).PubMed Central 
    Article 
    CAS 
    PubMed 

    Google Scholar 
    54.Held, N. L. & Whitaker, R. J. Viral biogeography revealed by signatures in Sulfolobus islandicus genomes. Environ. Microbiol. 11, 457–466 (2009).CAS 
    PubMed 
    Article 

    Google Scholar 
    55.Baquero, D. P. et al. New virus isolates from Italian hydrothermal environments underscore the biogeographic pattern in archaeal virus communities. ISME J. 14, 1821–1833 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    56.Molnár, J. et al. Identification of a novel archaea virus, detected in hydrocarbon polluted Hungarian and Canadian samples. PLoS ONE 15, e0231864 (2020).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    57.Prangishvili, D., Garrett, R. A. & Koonin, E. V. Evolutionary genomics of archaeal viruses: unique viral genomes in the third domain of life. Virus Res. 117, 52–67 (2006).CAS 
    PubMed 
    Article 

    Google Scholar 
    58.Deng, L., Garrett, R. A., Shah, S. A., Peng, X. & She, Q. A novel interference mechanism by a type IIIB CRISPR-Cmr module in Sulfolobus. Mol. Microbiol. 87, 1088–1099 (2013).CAS 
    PubMed 
    Article 

    Google Scholar 
    59.Silas, S. et al. Type III CRISPR-Cas systems can provide redundancy to counteract viral escape from type I systems. Elife 6, e27601 (2017).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    60.Guo, T., Han, W. & She, Q. Tolerance of Sulfolobus SMV1 virus to the immunity of IA and III-B CRISPR-Cas systems in Sulfolobus islandicus. RNA Biol. 16, 549–556 (2019).PubMed 
    Article 

    Google Scholar 
    61.Athukoralage, J. S. et al. An anti-CRISPR viral ring nuclease subverts type III CRISPR immunity. Nature 577, 572–575 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar 
    62.Bhoobalan-Chitty, Y., Johansen, T. B., Di Cianni, N. & Peng, X. Inhibition of type III CRISPR-Cas immunity by an archaeal virus-encoded anti-CRISPR protein. Cell 179, 448–458 e411 (2019).CAS 
    PubMed 
    Article 

    Google Scholar 
    63.Thingstad, T. F. & Lignell, R. Theoretical models for the control of bacterial growth rate, abundance, diversity and carbon demand. Aquat. Microbiol. Ecol. 13, 19–27 (1997).Article 

    Google Scholar 
    64.Wilhelm, S. W. & Suttle, C. A. Viruses and nutrient cycles in the sea—viruses play critical roles in the structure and function of aquatic food webs. Bioscience 49, 781–788 (1999).Article 

    Google Scholar 
    65.Probst, A. J. et al. Lipid analysis of CO2-rich subsurface aquifers suggests an autotrophy-based deep biosphere with lysolipids enriched in CPR bacteria. ISME J. 14, 1547–1560 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    66.Dong, X. et al. Fermentative spirochaetes mediate necromass recycling in anoxic hydrocarbon-contaminated habitats. ISME J. 12, 2039–2050 (2018).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    67.Vidakovic, L., Singh, P. K., Hartmann, R., Nadell, C. D. & Drescher, K. Dynamic biofilm architecture confers individual and collective mechanisms of viral protection. Nat. Microbiol. 3, 26–31 (2018).CAS 
    PubMed 
    Article 

    Google Scholar 
    68.Buchfink, B., Xie, C. & Huson, D. H. Fast and sensitive protein alignment using DIAMOND. Nat. Methods 12, 59–60 (2015).CAS 
    PubMed 
    Article 

    Google Scholar 
    69.Quast, C. et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41, D590–D596 (2013).CAS 
    PubMed 
    Article 

    Google Scholar 
    70.Probst, A. J. et al. Coupling genetic and chemical microbiome profiling reveals heterogeneity of archaeome and bacteriome in subsurface biofilms that are dominated by the same archaeal species. PLoS ONE 9, e99801 (2014).71.John, S. G. et al. A simple and efficient method for concentration of ocean viruses by chemical flocculation. Environ. Microbiol. Rep. 3, 195–202 (2011).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    72.Joshi, N. & Fass, J. Sickle: a sliding-window, adaptive, quality-based trimming tool for FastQ files (Version 1.33) [Software]. https://github.com/najoshi/sickle (2011).73.Nurk, S., Meleshko, D., Korobeynikov, A. & Pevzner, P. A. metaSPAdes: a new versatile metagenomic assembler. Genome Res. 27, 824–834 (2017).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    74.Hyatt, D. et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinform. 11, 119 (2010).Article 
    CAS 

    Google Scholar 
    75.Suzek, B. E., Huang, H., McGarvey, P., Mazumder, R. & Wu, C. H. UniRef: comprehensive and non-redundant UniProt reference clusters. Bioinformatics 23, 1282–1288 (2007).CAS 
    PubMed 
    Article 

    Google Scholar 
    76.Bornemann, T. L. V., Esser, S. P., Stach, T. L., Burg, T. & Probst, A.J. uBin—a manual refining tool for metagenomic bins designed for educational purposes. https://doi.org/10.1101/2020.07.15.204776 (2020).77.Couvin, D. et al. CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins. Nucleic Acids Res. 46, W246–W251 (2018).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    78.Medvedeva, S. et al. Virus-borne mini-CRISPR arrays are involved in interviral conflicts. Nat. Commun. 10, 5204 (2019).PubMed 
    PubMed Central 
    Article 
    ADS 
    CAS 

    Google Scholar 
    79.Iranzo, J., Faure, G., Wolf, Y. I. & Koonin, E. V. Game-theoretical modeling of interviral conflicts mediated by mini-CRISPR arrays. Front. Microbiol. 11, 381 (2020).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    80.Denman, R. B. Using Rnafold to predict the activity of small catalytic RNAs. Biotechniques 15, 1090-& (1993).
    Google Scholar 
    81.Lange, S. J., Alkhnbashi, O. S., Rose, D., Will, S. & Backofen, R. CRISPRmap: an automated classification of repeat conservation in prokaryotic adaptive immune systems. Nucleic Acids Res. 41, 8034–8044 (2013).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    82.Moller, A. G. & Liang, C. MetaCRAST: reference-guided extraction of CRISPR spacers from unassembled metagenomes. PeerJ 5, e3788 (2017).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    83.Li, W. & Godzik, A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22, 1658–1659 (2006).CAS 
    PubMed 
    Article 

    Google Scholar 
    84.Bischoff, V. et al. Cobaviruses—a new globally distributed phage group infecting Rhodobacteraceae in marine ecosystems. ISME J. 13, 1404–1421 (2019).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    85.Boratyn, G. M. et al. Domain enhanced lookup time accelerated BLAST. Biol. Direct 7, 12 (2012).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    86.Grazziotin, A. L., Koonin, E. V. & Kristensen, D. M. Prokaryotic virus orthologous groups (pVOGs): a resource for comparative genomics and protein family annotation. Nucleic Acids Res. 45, D491–D498 (2017).CAS 
    PubMed 
    Article 

    Google Scholar 
    87.Remmert, M., Biegert, A., Hauser, A. & Söding, J. HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nat. Methods 9, 173–175 (2011).PubMed 
    Article 
    CAS 

    Google Scholar 
    88.Marz, M. et al. Challenges in RNA virus bioinformatics. Bioinformatics 30, 1793–1799 (2014).CAS 
    PubMed 
    Article 

    Google Scholar 
    89.Finn, R. D. et al. InterPro in 2017-beyond protein family and domain annotations. Nucleic Acids Res. 45, D190–D199 (2017).CAS 
    PubMed 
    Article 

    Google Scholar 
    90.Kearse, M. et al. Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28, 1647–1649 (2012).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    91.Söding, J., Biegert, A. & Lupas, A. N. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res. 33, W244–W248 (2005).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    92.Zimmermann, L. et al. A completely reimplemented MPI bioinformatics toolkit with a new HHpred server at its core. J. Mol. Biol. 430, 2237–2243 (2018).CAS 
    PubMed 
    Article 

    Google Scholar 
    93.Potter, S. C. et al. HMMER web server: 2018 update. Nucleic Acids Res. 46, W200–W204 (2018).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    94.Meier-Kolthoff, J. P. & Göker, M. VICTOR: genome-based phylogeny and classification of prokaryotic viruses. Bioinformatics 33, 3396–3404 (2017).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    95.Meier-Kolthoff, J. P., Auch, A. F., Klenk, H. P. & Göker, M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform. 14, 60 (2013).Article 

    Google Scholar 
    96.Göker, M., Garcia-Blazquez, G., Voglmayr, H., Telleria, M. T. & Martin, M. P. Molecular taxonomy of phytopathogenic fungi: a case study in Peronospora. PLoS ONE 4, e6319 (2009).PubMed 
    PubMed Central 
    Article 
    ADS 
    CAS 

    Google Scholar 
    97.Bin Jang, H. et al. Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks. Nat. Biotechnol. 37, 632–639 (2019).Article 
    CAS 

    Google Scholar 
    98.Bolduc, B. et al. vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect archaea and bacteria. PeerJ 5, e3243 (2017).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    99.Brister, J. R., Ako-Adjei, D., Bao, Y. & Blinkova, O. NCBI viral genomes resource. Nucleic Acids Res. 43, D571–D577 (2015).CAS 
    Article 

    Google Scholar 
    100.Shannon, P. et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498–2504 (2003).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    101.Moraru, C., Varsani, A. & Kropinski, A. M. VIRIDIC-A novel tool to calculate the intergenomic similarities of prokaryote-infecting viruses. Viruses 12, 1268 (2020).102.Guy, L., Kultima, J. R. & Andersson, S. G. genoPlotR: comparative gene and genome visualization in R. Bioinformatics 26, 2334–2335 (2010).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    103.Team RC. R: a language and environment for statistical computing. (R Foundation for Statistical Computing, 2019). https://www.R-project.org/.104.Papadopoulos, J. S. & Agarwala, R. COBALT: constraint-based alignment tool for multiple protein sequences. Bioinformatics 23, 1073–1079 (2007).CAS 
    PubMed 
    Article 

    Google Scholar 
    105.Edgar, R. C. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinform. 5, 113 (2004).Article 
    CAS 

    Google Scholar 
    106.Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree 2—approximately maximum-likelihood trees for large alignments. PLoS ONE 5, e9490 (2010).PubMed 
    PubMed Central 
    Article 
    ADS 
    CAS 

    Google Scholar 
    107.Castresana, J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17, 540–552 (2000).CAS 
    PubMed 
    Article 

    Google Scholar 
    108.Guindon, S. et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 59, 307–321 (2010).CAS 
    PubMed 
    Article 

    Google Scholar 
    109.Rambaut, A. FigTree, a graphical viewer of phylogenetic trees and as a program for producing publication-ready figures. http://tree.bio.ed.ac.uk/software/figtree/ (2006).110.Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    111.Barrero-Canosa, J. & Moraru, C. Linking microbes to their genes at single cell level with direct-geneFISH. In: An Overview of FISH Concepts and Protocols for Microbial Cells (eds Almeida, C. & Azevedo, N.). (Springer Nature, 2020).112.Barrero-Canosa, J., Moraru, C., Zeugner, L., Fuchs, B. M. & Amann, R. Direct-geneFISH: a simplified protocol for the simultaneous detection and quantification of genes and rRNA in microorganisms. Environ. Microbiol. 19, 70–82 (2017).CAS 
    PubMed 
    Article 

    Google Scholar 
    113.Perras, A. K. et al. S-layers at second glance? Altiarchaeal grappling hooks (hami) resemble archaeal S-layer proteins in structure and sequence. Front. Microbiol. 6, 543 (2015).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    114.Wallner, G., Amann, R. & Beisker, W. Optimizing fluorescent in situ hybridization with rRNA-targeted oligonucleotide probes for flow cytometric identification of microorganisms. Cytometry 14, 136–143 (1993).CAS 
    PubMed 
    Article 

    Google Scholar 
    115.Moissl, C., Rudolph, C., Rachel, R., Koch, M. & Huber, R. In situ growth of the novel SM1 euryarchaeon from a string-of-pearls-like microbial community in its cold biotope, its physical separation and insights into its structure and physiology. Arch. Microbiol. 180, 211–217 (2003).CAS 
    PubMed 
    Article 

    Google Scholar 
    116.Flechsler, J. et al. 2D and 3D immunogold localization on (epoxy) ultrathin sections with and without osmium tetroxide. Microsc. Res. Tech. 83, 691–705 (2020).117.Schlitzer, R. Data Analysis and Visualization with Ocean Data View, CMOS Bulletin SCMO. 43, 9–13 (2015). More

  • in

    Earthworms drastically change fungal and bacterial communities during vermicomposting of sewage sludge

    The composition of bacterial and fungal microbiotas changes during vermicomposting of sewage sludgeThe bacterial community of the raw sewage sludge included 19 phyla and was mainly comprised of Bacteroidota, Bdellovibrionota, Campilobacterota, Firmicutes and Proteobacteria (Fig. 1). Bacterial communities of fresh earthworm casts were dominated by the phyla Bacteroidota, Proteobacteria and Verrucomicrobiota (Fig. 1). Large changes in bacterial community composition were found after transit of the sewage sludge through the gut of the earthworms (GAP), with significant decreases in the abundance of Campilobacterota, Firmicutes and Bacteroidota, and significant increases in the abundance of Verrucomicrobiota, Proteobacteria and Bacteroidota (Supplementary Table S1). At the genus level, transit through the gut significantly reduced the abundance of bacterial genera Terrimonas, Acetoanaerobium, Bacteroides, Cloacibacterium, Proteocatella and Macellibacteroides among others (Fig. 1, Supplementary Table S2), and increased significantly the abundance of Dyadobacter, Aeromonas, Luteolibacter, Edaphobaculum, Cellvibrio, Pedobacter, Sphingomonas, Devosia, Cetobacterium and Rhodanobacter among others (Fig. 1, Supplementary Table S2). At ASV level, transit through the earthworm gut significantly reduced the relative abundance of 49 bacterial ASVs and increased the relative abundance of 54 bacterial ASVs (Supplementary Table S3).Figure 1Relative abundance of the main phyla and genera of bacteria in sewage sludge, fresh earthworm casts and vermicompost (3 months old) during vermicomposting of sewage sludge. Low abundance bacterial phyla and genera ( More

  • in

    Male diet affects female fitness and sperm competition in human- and bat-associated lineages of the common bedbug, Cimex lectularius

    1.Coyne, J. A. & Orr, A. H. Speciation. (Sinauer associates, Inc., 2004).2.Nosil, P. Ecological speciation. (Oxford University Press, 2012). https://doi.org/10.1093/acprof:osobl/9780199587100.001.00013.Parker, G. A. Sperm competition and its evolutionary consequences in the insects. Biol. Rev. 45, 525–567 (1970).Article 

    Google Scholar 
    4.Almbro, M., Dowling, D. K. & Simmons, L. W. Effects of vitamin E and beta-carotene on sperm competitiveness. Ecol. Lett. 14, 891–895 (2011).PubMed 
    Article 

    Google Scholar 
    5.Sutter, A. & Immler, S. Within-ejaculate sperm competition. Philos. Trans. R. Soc. Lond. B. Biol. Sci. 375, 20200066 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    6.Balfour, V. L., Black, D. & Shuker, D. M. Mating failure shapes the patterns of sperm precedence in an insect. Behav. Ecol. Sociobiol. 74, 1–14 (2020).Article 

    Google Scholar 
    7.Reinhardt, K., Dobler, R. & Abbott, J. An ecology of sperm: Sperm diversification by natural selection. Annu. Rev. Ecol. Evol. Syst. 46, 435–459 (2015).Article 

    Google Scholar 
    8.Dobler, R. & Reinhardt, K. Heritability, evolvability, phenotypic plasticity and temporal variation in sperm-competition success of Drosophila melanogaster. J. Evol. Biol. 29, 929–941 (2016).CAS 
    PubMed 
    Article 

    Google Scholar 
    9.Evans, J. P., Lymbery, R. A., Wiid, K. S., Rahman, M. M. & Gasparini, C. Sperm as moderators of environmentally induced paternal effects in a livebearing fish. Biol. Lett. 13, 20170087 (2017).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    10.Alavi, S. M. H. & Cosson, J. Sperm motility in fishes. I. Effects of temperature and pH: A review. Cell Biol. Int. 29, 101–110 (2005).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    11.Foresta, C. et al. Human papillomavirus found in sperm head of young adult males affects the progressive motility. Fertil. Steril. 93, 802–806 (2010).PubMed 
    Article 

    Google Scholar 
    12.Mann, T. The biochemistry of semen and the male reproductive tract. (London: Methuen & Co (1964), 1964).13.Otti, O., McTighe, A. P. & Reinhardt, K. In vitro antimicrobial sperm protection by an ejaculate-like substance. Funct. Ecol. 27, 219–226 (2013).Article 

    Google Scholar 
    14.Valdebenito, I., Fletcher, C., Vera, V. & Fernández, J. Physical-chemical factors that regulate spermatic motility in fish: Basic and applied aspects. A review. . Arch. Med. Vet. 41, 97–106 (2009).CAS 
    Article 

    Google Scholar 
    15.Werner, M. & Simmons, L. W. Insect sperm motility. Biol. Rev. 83, 191–208 (2008).PubMed 
    Article 

    Google Scholar 
    16.Barros, C. M., Pegorer, M. F., Vasconcelos, J. L. M., Eberhardt, B. G. & Monteiro, F. M. Importance of sperm genotype (indicus versus taurus) for fertility and embryonic development at elevated temperatures. Theriogenology 65, 210–218 (2006).PubMed 
    Article 

    Google Scholar 
    17.Blanco, J. M., Gee, G., Wildt, D. E. & Donoghue, A. M. Species variation in osmotic, cryoprotectant, and cooling rate tolerance in poultry, eagle, and peregrine falcon spermatozoa. Biol. Reprod. 63, 1164–1171 (2000).CAS 
    PubMed 
    Article 

    Google Scholar 
    18.Chacur, M. G. M., Mizusaki, K. T., Filho, L. R. A. G., Oba, E. & Ramos, A. A. Seasonal effects on semen and testosterone in zebu and taurine bulls. Acta Sci. Vet. 41, 1110 (2013).
    Google Scholar 
    19.Lewis, S. M., Tigreros, N., Fedina, T. & Ming, Q. L. Genetic and nutritional effects on male traits and reproductive performance in Tribolium flour beetles. J. Evol. Biol. 25, 438–451 (2012).CAS 
    PubMed 
    Article 

    Google Scholar 
    20.Schramm, G.-P. Studies on genotype specific modified methods for cryopreservation of cock semen. Züchtungskunde 80, 137–145 (2008).
    Google Scholar 
    21.Rohmer, C., David, J. R., Moreteau, B. & Joly, D. Heat induced male sterility in Drosophila melanogaster: Adaptive genetic variations among geographic populations and role of the Y chromosome. J. Exp. Biol. 207, 2735–2743 (2004).PubMed 
    Article 

    Google Scholar 
    22.Reinhardt, K. & Otti, O. Comparing sperm swimming speed. Evol. Ecol. Res. 14, 1–8 (2012).
    Google Scholar 
    23.Öst, A. et al. Paternal diet defines offspring chromatin state and intergenerational obesity. Cell 159, 1352–1364 (2014).PubMed 
    Article 
    CAS 

    Google Scholar 
    24.Wathes, D. C., Abayasekara, D. R. E. & Aitken, R. J. Polyunsaturated fatty acids in male and female reproduction. Biol. Reprod. 77, 190–201 (2007).CAS 
    PubMed 
    Article 

    Google Scholar 
    25.Diaz-Fontdevila, M. & Bustos-Obregon, E. Cholesterol and polyunsaturated acid enriched diet: Effect on kinetics of the acrosome reaction in rabbit spermatozoa. Mol. Reprod. Dev. 35, 176–180 (1993).CAS 
    PubMed 
    Article 

    Google Scholar 
    26.Keber, R., Rozman, D. & Horvat, S. Sterols in spermatogenesis and sperm maturation. J. Lipid Res. 54, 20–33 (2013).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    27.Guo, R. & Reinhardt, K. Dietary polyunsaturated fatty acids affect volume and metabolism of Drosophila melanogaster sperm. J. Evol. Biol. https://doi.org/10.1111/jeb.13591 (2020).Article 
    PubMed 

    Google Scholar 
    28.Rato, L., Alves, M. G., Cavaco, J. E. & Oliveira, P. F. High-energy diets: a threat for male fertility?. Obes. Rev. 15, 996–1007 (2014).CAS 
    PubMed 
    Article 

    Google Scholar 
    29.Ferramosca, A., Moscatelli, N., Di Giacomo, M. & Zara, V. Dietary fatty acids influence sperm quality and function. Andrology 5, 423–430 (2017).CAS 
    PubMed 
    Article 

    Google Scholar 
    30.Paynter, E. et al. Insights into the molecular basis of long-term storage and survival of sperm in the honeybee (Apis mellifera). Sci. Rep. 7, 1–9 (2017).Article 
    CAS 

    Google Scholar 
    31.Chinoy, N. J., Mehta, D. & Jhala, D. Effects of fluoride ingestion with protein deficient or protein enriched diets on sperm function of mice. Fluoride 39, 11–16 (2006).CAS 

    Google Scholar 
    32.Watkins, A. J. et al. Paternal diet programs offspring health through sperm- and seminal plasma-specific pathways in mice. Proc. Natl. Acad. Sci. U. S. A. 115, 10064–10069 (2018).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    33.Ferramosca, A. & Zara, V. Bioenergetics of mammalian sperm capacitation. Biomed Res. Int. 2014, 902953 (2014).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    34.Vawda, A. I. & Mandlwana, J. G. The effects of dietary protein deficiency on rat testicular function. Andrologia 22, 575–583 (1990).CAS 
    PubMed 
    Article 

    Google Scholar 
    35.Carvalho, M. et al. Effects of diet and development on the Drosophila lipidome. Mol. Syst. Biol. 8, 600 (2012).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    36.Macartney, E. L., Crean, A. J., Nakagawa, S. & Bonduriansky, R. Effects of nutrient limitation on sperm and seminal fluid: a systematic review and meta-analysis. Biol. Rev. 94, 1722–1739 (2019).PubMed 
    Article 

    Google Scholar 
    37.Avila, F. W., Sirot, L. K., LaFlamme, B. A., Rubinstein, C. D. & Wolfner, M. F. Insect seminal fluid proteins: Identification and function. Annu. Rev. Entomol. 56, 21–40 (2011).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    38.Wainwright, M. S. et al. Drosophila Sex Peptide controls the assembly of lipid microcarriers in seminal fluid. Proc. Natl. Acad. Sci. USA 118, e2019622118 (2021).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    39.Elofsson, H., Van Look, K., Borg, B. & Mayer, I. Influence of salinity and ovarian fluid on sperm motility in the fifteen-spined stickleback. J. Fish Biol. 63, 1429–1438 (2003).Article 

    Google Scholar 
    40.Otti, O., Johnston, P. R., Horsburgh, G. J., Galindo, J. & Reinhardt, K. Female transcriptomic response to male genetic and nongenetic ejaculate variation. Behav. Ecol. 26, 681–688 (2015).Article 

    Google Scholar 
    41.Balvín, O., Munclinger, P., Kratochvíl, L. & Vilímová, J. Mitochondrial DNA and morphology show independent evolutionary histories of bedbug Cimex lectularius (Heteroptera: Cimicidae) on bats and humans. Parasitol. Res. 111, 457–469 (2012).PubMed 
    Article 

    Google Scholar 
    42.Booth, W., Balvín, O., Vargo, E. L., Vilímová, J. & Schal, C. Host association drives genetic divergence in the bed bug. Cimex lectularius. Mol. Ecol. 24, 980–992 (2015).PubMed 
    Article 

    Google Scholar 
    43.Wawrocka, K. & Bartonička, T. Two different lineages of bedbug (Cimex lectularius) reflected in host specificity. Parasitol. Res. 112, 3897–3904 (2013).PubMed 
    Article 

    Google Scholar 
    44.Aak, A. & Rukke, B. A. Bed bugs, their blood sources and life history parameters: A comparison of artificial and natural feeding. Med. Vet. Entomol. 28, 50–59 (2014).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    45.Reinhardt, K., Naylor, R. & Siva-Jothy, M. T. Reducing a cost of traumatic insemination: Female bedbugs evolve a unique organ. Proc. R. Soc. B Biol. Sci. 270, 2371–2375 (2003).Article 

    Google Scholar 
    46.Reinhardt, K., Naylor, R. A. & Siva-Jothy, M. T. Situation exploitation: Higher male mating success when female resistance is reduced by feeding. Evolution (N. Y.). 63, 29–39 (2009).
    Google Scholar 
    47.Siva-Jothy, M. T. & Stutt, A. D. A matter of taste: Direct detection of female mating status in the bedbug. Proc. R. Soc. B Biol. Sci. 270, 649–652 (2003).Article 

    Google Scholar 
    48.Davis, N. T. Studies of the reproductive physiology of Cimicidae (Hemiptera)-II. Artificial insemination and the function of the seminal fluid. J. Insect. Physiol. 11, 355–366 (1965).Article 

    Google Scholar 
    49.Kaldun, B. & Otti, O. Condition-dependent ejaculate production affects male mating behavior in the common bedbug Cimex lectularius. Ecol. Evol. 6, 2548–2558 (2016).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    50.Reinhardt, K., Naylor, R. A. & Siva-Jothy, M. T. Ejaculate components delay reproductive senescence while elevating female reproductive rate in an insect. Proc. Natl. Acad. Sci. USA 106, 21743–21747 (2009).CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar 
    51.Reinhardt, K., Naylor, R. & Siva-Jothy, M. T. Male mating rate is constrained by seminal fluid availability in bedbugs, Cimex lectularius. . PLoS ONE 6, 282 (2011).Article 
    CAS 

    Google Scholar 
    52.Fountain, T., Duvaux, L., Horsburgh, G., Reinhardt, K. & Butlin, R. K. Human-facilitated metapopulation dynamics in an emerging pest species. Cimex lectularius. Mol. Ecol. 23, 1071–1084 (2014).PubMed 
    Article 

    Google Scholar 
    53.R Core Team. R: A language and environment for statistical computing. (2020).54.Bates, D., Maechler, M., Bolker, B. & Walker, S. Fitting linear mixed-effects models using lme4. J. Stat. Softw. 67, 1–48 (2015).Article 

    Google Scholar 
    55.Kuznetsova, A., Brockhoff, P. B. & Christensen, R. H. B. lmerTest package: Tests in linear mixed effects models. J. Stat. Softw. 82, 1–26 (2017).Article 

    Google Scholar 
    56.Brooks, M. E. et al. glmmTMB balances speed and flexibility among packages for zero-inflated generalized linear mixed modeling. R J. 9, 378–400 (2017).Article 

    Google Scholar 
    57.Therneau, T. M. coxme: Mixed effects cox models. (2019).58.Harrison, X. A. A comparison of observation-level randomeffect and Beta-Binomial models for modelling overdispersion in Binomial data in ecology & evolution. PeerJ 2015, 114 (2015).
    Google Scholar 
    59.Clark, A. G., Aguadé, M., Prout, T. R., Harshman, L. G. & Langley, C. H. Variation in sperm displacement and its association with accessory gland protein loci in Drosophila melanogaster. Genetics 139, 189–201 (1995).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    60.Friberg, U., Lew, T. A., Byrne, P. G. & Rice, W. R. Assessing the potential for an ongoing arms race within and between the sexes: selection and heritable variation. Evol. (N.Y.) 59, 1540 (2005).
    Google Scholar 
    61.Morimoto, J. & Wigby, S. Differential effects of male nutrient balance on pre-and post-copulatory traits, and consequences for female reproduction in Drosophila melanogaster. Sci. Rep. 6, 27673 (2016).CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar 
    62.Rahman, M. M., Gasparini, C., Turchini, G. M. & Evans, J. P. Experimental reduction in dietary omega-3 polyunsaturated fatty acids depresses sperm competitiveness. Biol. Lett. 10, 20140623 (2014).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    63.Hawkey, C. M. Comparative mammalian haematology : cellular components and blood coagulation of captive wild animals. (Butterworth-Heinemann, 2017).64.Wawrocka, K. & Bartonička, T. Erythrocyte size as one of potential causes of host preferences in cimicids (Heteroptera: Cimicidae: Cimex). Vespertilio 17, 215–220 (2014).
    Google Scholar 
    65.Bunning, H. et al. Protein and carbohydrate intake influence sperm number and fertility in male cockroaches, but not sperm viability. Proc. R. Soc. B Biol. Sci. 282, 1 (2015).CAS 

    Google Scholar 
    66.Perez-Staples, D., Harmer, A. M. T., Collins, S. R. & Taylor, P. W. Potential for pre-release diet supplements to increase the sexual performance and longevity of male Queensland fruit flies. Agric. For. Entomol. 10, 255–262 (2008).Article 

    Google Scholar 
    67.Dàvila, F. & Aron, S. Protein restriction affects sperm number but not sperm viability in male ants. J. Insect. Physiol. 100, 71–76 (2017).PubMed 
    Article 
    CAS 

    Google Scholar 
    68.Olsen, J. & Ramlau-Hansen, C. H. Dietary fats may impact semen quantity and quality. Asian J. Androl. 14, 511–512 (2012).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    69.Birkhead, T. R., Martínez, J. G., Burke, T. & Froman, D. P. Sperm mobility determines the outcome of sperm competition in the domestic fowl. Proc. R. Soc. B Biol. Sci. 266, 1759–1764 (1999).CAS 
    Article 

    Google Scholar 
    70.Colegrave, N., Birkhead, T. R. & Lessells, C. M. Sperm precedence in zebra finches does not require special mechanisms of sperm competition. Proc. R. Soc. B Biol. Sci. 259, 223–228 (1995).Article 
    ADS 

    Google Scholar 
    71.Simmons, L. W. Sperm competition and its evolutionary consequences in the insects. (Princeton University Press, 2001).72.Tsubaki, Y. & Yamagishi, M. ‘Longevity’ of sperm within the female of the melon fly, Dacus cucurbitae (Diptera: Tephritidae), and its relevance to sperm competition. J. Insect. Behav. 4, 243–250 (1991).Article 

    Google Scholar 
    73.Yamagishi, M., Itô, Y. & Tsubaki, Y. Sperm competition in the melon fly, Bactrocera cucurbitae (Diptera: Tephritidae): Effects of sperm ‘longevity’ on sperm precedence. J. Insect. Behav. 5, 599–608 (1992).Article 

    Google Scholar 
    74.Reinhardt, K. Evolutionary consequences of sperm cell aging. Q. Rev. Biol. 82, 375–393 (2007).PubMed 
    Article 

    Google Scholar 
    75.Frankham, R. & Ralls, K. Inbreeding leads to extinction. Nature 392, 441–442 (1998).CAS 
    Article 
    ADS 

    Google Scholar  More