Phage strategies facilitate bacterial coexistence under environmental variability
Bacterial communities are often exposed to temporal variations in resource availability, which exceed bacterial generation times and thereby affect bacterial coexistence. Bacterial population dynamics are also shaped by bacteriophages, which are a main cause of bacterial mortality. Several strategies are proposed in the literature to describe infections by phages, such as “Killing the Winner”, “Piggyback the loser” (PtL) or “Piggyback the Winner” (PtW). The two temperate phage strategies PtL and PtW are defined by a change from lytic to lysogenic infection when the host density changes, from high to low or from low to high, respectively. To date, the occurrence of different phage strategies and their response to environmental variability is poorly understood. In our study, we developed a microbial trophic network model using ordinary differential equations (ODEs) and performed ‘in silico’ experiments. To model the switch from the lysogenic to the lytic cycle, we modified the lysis rate of infected bacteria and their growth was turned on or off using a density-dependent switching point. We addressed whether and how the different phage strategies facilitate bacteria coexistence competing for limiting resources. We also studied the impact of a fluctuating resource inflow to evaluate the response of the different phage strategies to environmental variability. Our results show that the viral shunt (i.e. nutrient release after bacterial lysis) leads to an enrichment of the system. This enrichment enables bacterial coexistence at lower resource concentrations. We were able to show that an established, purely lytic model leads to stable bacterial coexistence despite fluctuating resources. Both temperate phage models differ in their coexistence patterns. The model of PtW yields stable bacterial coexistence at a limited range of resource supply and is most sensitive to resource fluctuations. Interestingly, the purely lytic phage strategy and PtW both result in stable bacteria coexistence at oligotrophic conditions. The PtL model facilitates stable bacterial coexistence over a large range of stable and fluctuating resource inflow. An increase in bacterial growth rate results in a higher resilience to resource variability for the PtL and the lytic infection model. We propose that both temperate phage strategies represent different mechanisms of phages coping with environmental variability. Our study demonstrates how phage strategies can maintain bacterial coexistence in constant and fluctuating environments.
Voigt et al. (2021) Phage strategies facilitate bacterial coexistence under environmental variability. PeerJ 9:e12194 https://doi.org/10.7717/peerj.12194
Courtship behavior and identification of a sex pheromone in Ibalia leucospoides (Hymenoptera: Ibaliidae), a larval parasitoid of Sirex noctilio (Hymenoptera: Siricidae)
Background Ibalia leucospoides (Hymenoptera: Ibaliidae) is a larval parasitoid that has been widely introduced as a biological control agent for the invasive woodwasp,Sirex noctilio (Hymenoptera: Siricidae) in the Southern Hemisphere. In this study, the courtship behavior and identificaion of sex pheromones are described for I. leucospoides under laboratory conditions. Methods For courtship behavior, both sexes were observed in a wire mesh observation cylinder (75 cm length ×10 cm diameter) for 15 minutes. The female body washes were analyzed using Gas Chromatography- Electroantennographic Detection (GC-EAD). Then the EAD-active compounds were tentatively identified using GC-Mass Spectrometry (GC-MS) and examined in olfactometer assays. Results The courtship behavior included rhythmic lateral movements, mounting, head-nodding cycles in males, and wing-fanning in females. GC-EAD analysis of female body washes with male antennae revealed seven compounds which elicited antennal responses, four of which are straight-chain alkanes (C23, C25, C26, and C27). The identities of these alkanes were confirmed by matching the retention times, mass spectra, and male antennal activity to those of commercially obtained chemicals. In olfactometer assays, a blend of the four straight-chain alkanes was attractive to I. leucospoides males, and there was no response to blends that lacked any of these four compounds. Female body wash was no more attractive than the four-component blend. The ratios of EAD-active components differ between hydrocarbon profiles from males and females. Conclusion This study is the first investigation of cuticular hydrocarbons in the family Ibaliidae. It provides evidence that the ubiquitous alkanes (C23, C25, C26, and C27) in sex-specific ratios attract I. leucospoides males.
Faal et al. (2021) Courtship behavior and identification of a sex pheromone in Ibalia leucospoides (Hymenoptera: Ibaliidae), a larval parasitoid of Sirex noctilio (Hymenoptera: Siricidae). PeerJ 9:e12266 https://doi.org/10.7717/peerj.12266
Spatial and temporal dynamics of SAR11 marine bacteria across a nearshore to offshore transect in the tropical Pacific Ocean
Surveys of microbial communities across transitions coupled with contextual measures of the environment provide a useful approach to dissect the factors determining distributions of microorganisms across ecological niches. Here, monthly time-series samples of surface seawater along a transect spanning the nearshore coastal environment within Kāneʻohe Bay on the island of Oʻahu, Hawaiʻi, and the adjacent offshore environment were collected to investigate the diversity and abundance of SAR11 marine bacteria (order Pelagibacterales) over a 2-year time period. Using 16S ribosomal RNA gene amplicon sequencing, the spatiotemporal distributions of major SAR11 subclades and exact amplicon sequence variants (ASVs) were evaluated. Seven of eight SAR11 subclades detected in this study showed distinct subclade distributions across the coastal to offshore environments. The SAR11 community was dominated by seven (of 106 total) SAR11 ASVs that made up an average of 77% of total SAR11. These seven ASVs spanned five different SAR11 subclades (Ia, Ib, IIa, IV, and Va), and were recovered from all samples collected from either the coastal environment, the offshore, or both. SAR11 ASVs were more often restricted spatially to coastal or offshore environments (64 of 106 ASVs) than they were shared among coastal, transition, and offshore environments (39 of 106 ASVs). Overall, offshore SAR11 communities contained a higher diversity of SAR11 ASVs than their nearshore counterparts, with the highest diversity within the little-studied subclade IIa. This study reveals ecological differentiation of SAR11 marine bacteria across a short physiochemical gradient, further increasing our understanding of how SAR11 genetic diversity partitions into distinct ecological units.
Tucker et al. (2021) Spatial and temporal dynamics of SAR11 marine bacteria across a nearshore to offshore transect in the tropical Pacific Ocean. PeerJ 9:e12274 https://doi.org/10.7717/peerj.12274
Relationships between environmental variables and spatial and temporal distribution of jack mackerel (Trachurus japonicus) in the Beibu Gulf, South China Sea
The jack mackerel (Trachurus japonicus) is both a dominant pelagic fish species and an important fishing target in the Beibu Gulf, South China Sea. However, the resource status of this species fluctuates dramatically, and it has recently been added to a “red list” of threatened species of the International Union for Conservation of Nature (IUCN). Despite its economic importance and decreasing population status, limited research on its spatiotemporal distribution has been undertaken over the last decades. In order to evaluate the most crucial factors that influence the spatiotemporal variability of T. japonicus and to determine GAM performance and predictability, we analyze catch per unit effort (CPUE) of T. japonicus from Beibu Gulf over four seasons (months) from 2013 to 2014. A generalized additive model (GAMs) is populated with water depth and remotely sensed sea surface temperature (SST), sea surface salinity (SSS), sea surface chlorophyll-a concentration (Chl-a) and sea level anomaly (SLA). The CPUE of T. japonicus varies seasonally, with higher CPUE in summer and autumn than in spring and winter, and the highest CPUE in summer. GAM results explain 57% of the deviation explained in CPUE, with the most important variables being SLA, Month, Depth, SSS, and SST , each explaining 21.2%, 18.7%, 10.7%, 5.1%, and 1.3% of the variation in CPUE, respectively. This species occurs mainly between 50 and 75 m depth, SSS values 32.3–33.5 PSU and SST 25–30.5 °C. High CPUE sites occur near SLA ≤ 0 m, on the edge of cold eddies, and there is a certain catch near the sea surface with SLA ≥ 0 m. The spatial and temporal distribution of T. japonicus is affected by the season and the marine hydrological environment. This study might contribute to a better understanding of the distributional patterns of T. japonicus as well as provide a basis for sustainable management in the Beibu Gulf.
Feng et al. (2021) Relationships between environmental variables and spatial and temporal distribution of jack mackerel (Trachurus japonicus) in the Beibu Gulf, South China Sea. PeerJ 9:e12337 https://doi.org/10.7717/peerj.12337
Global gap-analysis of amphipod barcode library
In the age of global climate change and biodiversity loss there is an urgent need to provide effective and robust tools for diversity monitoring. One of the promising techniques for species identification is the use of DNA barcoding, that in Metazoa utilizes the so called ‘gold-standard’ gene of cytochrome c oxidase (COI). However, the success of this method relies on the existence of trustworthy barcode libraries of the species. The Barcode of Life Data System (BOLD) aims to provide barcodes for all existing organisms, and is complemented by the Barcode Index Number (BIN) system serving as a tool for potential species recognition. Here we provide an analysis of all public COI sequences available in BOLD of the diverse and ubiquitous crustacean order Amphipoda, to identify the barcode library gaps and provide recommendations for future barcoding studies. Our gap analysis of 25,702 records has shown that although 3,835 BINs (indicating putative species) were recognised by BOLD, only 10% of known amphipod species are represented by barcodes. We have identified almost equal contribution of both records (sequences) and BINs associated with freshwater and with marine realms. Three quarters of records have a complete species-level identification provided, while BINs have just 50%. Large disproportions between identification levels of BINs coming from freshwaters and the marine environment were observed, with three quarters of the former possessing a species name, and less than 40% for the latter. Moreover, the majority of BINs are represented by a very low number of sequences rendering them unreliable according to the quality control system. The geographical coverage is poor with vast areas of Africa, South America and the open ocean acting as “white gaps”. Several, of the most species rich and highly abundant families of Amphipoda (e.g., Phoxocephalidae, Ampeliscidae, Caprellidae), have very poor representation in the BOLD barcode library. As a result of our study we recommend stronger effort in identification of already recognised BINs, prioritising the studies of families that are known to be important and abundant components of particular communities, and targeted sampling programs for taxa coming from geographical regions with the least knowledge.
Jażdżewska et al. (2021) Global gap-analysis of amphipod barcode library. PeerJ 9:e12352 https://doi.org/10.7717/peerj.12352
Development and validation of a nomogram to predict postoperative pulmonary complications following thoracoscopic surgery
Background Postoperative pulmonary complications (PPCs) after thoracoscopic surgery are common. This retrospective study aimed to develop a nomogram to predict PPCs in thoracoscopic surgery. Methods A total of 905 patients who underwent thoracoscopy were randomly enrolled and divided into a training cohort and a validation cohort at 80%:20%. The training cohort was used to develop a nomogram model, and the validation cohort was used to validate the model. Univariate and multivariable logistic regression were applied to screen risk factors for PPCs, and the nomogram was incorporated in the training cohort. The discriminative ability and calibration of the nomogram for predicting PPCs were assessed using C-indices and calibration plots. Results Among the patients, 207 (22.87%) presented PPCs, including 166 cases in the training cohort and 41 cases in the validation cohort. Using backward stepwise selection of clinically important variables with the Akaike information criterion (AIC) in the training cohort, the following seven variables were incorporated for predicting PPCs: American Society of Anesthesiologists (ASA) grade III/IV, operation time longer than 180 min, one-lung ventilation time longer than 60 min, and history of stroke, heart disease, chronic obstructive pulmonary disease (COPD) and smoking. With incorporation of these factors, the nomogram achieved good C-indices of 0.894 (95% confidence interval (CI) [0.866–0.921]) and 0.868 (95% CI [0.811–0.925]) in the training and validation cohorts, respectively, with well-fitted calibration curves. Conclusion The nomogram offers good predictive performance for PPCs after thoracoscopic surgery. This model may help distinguish the risk of PPCs and make reasonable treatment choices.
Wang et al. (2021) Development and validation of a nomogram to predict postoperative pulmonary complications following thoracoscopic surgery. PeerJ 9:e12366 https://doi.org/10.7717/peerj.12366
A chimeric vector for dual use in cyanobacteria and Escherichia coli, tested with cystatin, a nonfluorescent reporter protein
Background Developing sustainable autotrophic cell factories depends heavily on the availability of robust and well-characterized biological parts. For cyanobacteria, these still lag behind the more advanced E. coli toolkit. In the course of previous protein expression experiments with cyanobacteria, we encountered inconveniences in working with currently available RSF1010-based shuttle plasmids, particularly due to their low biosafety and low yields of recombinant proteins. We also recognized some drawbacks of the commonly used fluorescent reporters, as quantification can be affected by the intrinsic fluorescence of cyanobacteria. To overcome these drawbacks, we envisioned a new chimeric vector and an alternative reporter that could be used in cyanobacterial synthetic biology and tested them in the model cyanobacterium Synechocystis sp. PCC 6803. Methods We designed the pMJc01 shuttle plasmid based on the broad host range RSFmob-I replicon. Standard cloning techniques were used for vector construction following the RFC10 synthetic biology standard. The behavior of pMJC01 was tested with selected regulatory elements in E. coli and Synechocystis sp. PCC 6803 for the biosynthesis of the established GFP reporter and of a new reporter protein, cystatin. Cystatin activity was assayed using papain as a cognate target. Results With the new vector we observed a significantly higher GFP expression in E. coli and Synechocystis sp. PCC 6803 compared to the commonly used RSF1010-based pPMQAK1. Cystatin, a cysteine protease inhibitor, was successfully expressed with the new vector in both E. coli and Synechocystis sp. PCC 6803. Its expression levels allowed quantification comparable to the standardly used fluorescent reporter GFPmut3b. An important advantage of the new vector is its improved biosafety due to the absence of plasmid regions encoding conjugative transfer components. The broadhost range vector pMJc01 could find application in synthetic biology and biotechnology of cyanobacteria due to its relatively small size, stability and ease of use. In addition, cystatin could be a useful reporter in all cell systems that do not contain papain-type proteases and inhibitors, such as cyanobacteria, and provides an alternative to fluorescent reporters or complements them.
Juteršek et al. (2021) A chimeric vector for dual use in cyanobacteria and Escherichia coli, tested with cystatin, a nonfluorescent reporter protein. PeerJ 9:e12199 https://doi.org/10.7717/peerj.12199
A comparison of diceCT and histology for determination of nasal epithelial type
Diffusible iodine-based contrast-enhanced computed tomography (diceCT) has emerged as a viable tool for discriminating soft tissues in serial CT slices, which can then be used for three-dimensional analysis. This technique has some potential to supplant histology as a tool for identification of body tissues. Here, we studied the head of an adult fruit bat (Cynopterus sphinx) and a late fetal vampire bat (Desmodus rotundus) using diceCT and µCT. Subsequently, we decalcified, serially sectioned and stained the same heads. The two CT volumes were rotated so that the sectional plane of the slice series closely matched that of histological sections, yielding the ideal opportunity to relate CT observations to corresponding histology. Olfactory epithelium is typically thicker, on average, than respiratory epithelium in both bats. Thus, one investigator (SK), blind to the histological sections, examined the diceCT slice series for both bats and annotated changes in thickness of epithelium on the first ethmoturbinal (ET I), the roof of the nasal fossa, and the nasal septum. A second trial was conducted with an added criterion: radioopacity of the lamina propria as an indicator of Bowman’s glands. Then, a second investigator (TS) annotated images of matching histological sections based on microscopic observation of epithelial type, and transferred these annotations to matching CT slices. Measurements of slices annotated according to changes in epithelial thickness alone closely track measurements of slices based on histologically-informed annotations; matching histological sections confirm blind annotations were effective based on epithelial thickness alone, except for a patch of unusually thick non-OE, mistaken for OE in one of the specimens. When characteristics of the lamina propria were added in the second trial, the blind annotations excluded the thick non-OE. Moreover, in the fetal bat the use of evidence for Bowman’s glands improved detection of olfactory mucosa, perhaps because the epithelium itself was thin enough at its margins to escape detection. We conclude that diceCT can by itself be highly effective in identifying distribution of OE, especially where observations are confirmed by histology from at least one specimen of the species. Our findings also establish that iodine staining, followed by stain removal, does not interfere with subsequent histological staining of the same specimen.
Smith et al. (2021) A comparison of diceCT and histology for determination of nasal epithelial type. PeerJ 9:e12261 https://doi.org/10.7717/peerj.12261
The predictive role of preoperative serum glutamate dehydrogenase levels in microvascular invasion and hepatocellular carcinoma prognosis following liver transplantation—a single center retrospective study
Background As a critical metabolic substrate, glutamine is not only involved in the progression of many cancers but is also related to angiogenesis. Glutamate dehydrogenase (GLDH), a key enzyme in glutamine metabolism, has been reported to regulate tumor proliferation; however, its relationship with microvascular invasion (MVI) is unclear. This study evaluated the ability of preoperative serum GLDH levels to predict MVI and the long-term survival of hepatocellular carcinoma (HCC) patients after liver transplantation (LT). Methods HCC patients that underwent LT from January 2015 to May 2020 at the First Affiliated Hospital of Sun Yat-Sen University were enrolled in our retrospective analysis. Clinicopathological variables were extracted from medical records. A receiver operating characteristic curve was created to determine the optimal cut-off value of GLDH for MVI. Results Preoperative GLDH was significantly elevated in the MVI-positive group (U = 454.00, p = 0.000). The optimal cut-off value of GLDH for MVI was 7.45 U/L, with an area under the curve of 0.747 (95% CI [0.639–0.856], p = 0.000). The sensitivity was 79.3%, while the specificity was 64.5%. GLDH > 7.45 U/L (p = 0.023) and maximum diameter >5 cm (p = 0.001) were independent risk factors for the presence of MVI. Patients with GLDH > 7.45 U/L had significantly poorer overall survival (p = 0.001) and recurrence-free survival (p = 0.001) after LT than patients with GLDH ≤ 7.45 U/L. Similarly, patients with MVI were associated with poor survival (p = 0.000). Conclusions Preoperative elevated serum GLDH levels predict MVI and poorer long-term survival for HCC after LT.
Gong et al. (2021) The predictive role of preoperative serum glutamate dehydrogenase levels in microvascular invasion and hepatocellular carcinoma prognosis following liver transplantation—a single center retrospective study. PeerJ 9:e12420 https://doi.org/10.7717/peerj.12420
Heavy metal pollution characteristics and health risk assessment of dust fall related to industrial activities in desert steppes
China’s desert steppe is the transition zone between the grasslands in central China and the arid desert. Ecological security in this region has long been a subject of debate, both in the local and academic communities. Heavy metals and other pollutants are readily released during industrial production, combustion, and transportation, aggravating the vulnerability of the desert steppes. To understand the impact of industrial activiteis on the heavy metal content of dust fall in the desert steppe, a total of 37 dust fall samples were collected over 90 days. An inductively-coupled plasma mass spectrometer (NexION 350X) was used to measure the concentration of heavy metals Cu, Cd, Cr, Pb, Mn, Co, and Zn in the dust. Using comprehensive pollution index and multivariate statistical analysis methods, we explored the characteristics and sources of heavy metal pollution. We also quantitatively assessed the carcinogenic risks of heavy metals resulting from dust reduction with the help of health risk assessment models. The heavy metals’ comprehensive pollution index values in the study area’s dust fall were ranked as follows: Zn > Cd > Pb > Mn > Cu > Co > Cr. Among these, Zn, Cd, and Pb were significant pollution factors in the study area, and were affected by industrial production and transportation. The high pollution index was concentrated in the north of the research industrial park and on both sides of a highway. The seven heavy metals’ total non-carcinogenic risk index (HI) values were ranked as follows: Mn > Co > Pb > Zn > Cr > Cu > Cd (only the HI of Mn was greater than one). Excluding Mn, the non-carcinogenic and carcinogenic risk index values of the other six heavy metals were within acceptable ranges. Previous studies have also shown that industrial transportation and production have had a significant impact on the heavy metal content of dust fall in the desert steppe.
Environmental Contamination and Remediation
Spatial and Geographic Information Science
Xu et al. (2021) Heavy metal pollution characteristics and health risk assessment of dust fall related to industrial activities in desert steppes. PeerJ 9:e12430 https://doi.org/10.7717/peerj.12430