Microbial regulation of soil carbon properties under nitrogen addition and plant inputs removal
Background Soil microbial communities and their associated enzyme activities play key roles in carbon cycling in terrestrial ecosystems. Soil microbial communities are sensitive to resource availability, but the mechanisms of microbial regulation have not been thoroughly investigated. Here, we tested the mechanistic relationships between microbial responses and multiple interacting resources. Methods We examined soil carbon properties, soil microbial community structure and carbon-related functions under nitrogen addition and plant inputs removal (litter removal (NL), root trench and litter removal (NRL)) in a pure Larix principis-rupprechtii plantation in northern China. Results We found that nitrogen addition affected the soil microbial community structure, and that microbial biomass increased significantly once 100 kg ha−1 a−1 of nitrogen was added. The interactions between nitrogen addition and plant inputs removal significantly affected soil bacteria and their enzymatic activities (oxidases). The NL treatment enhanced soil microbial biomass under nitrogen addition. We also found that the biomass of gram-negative bacteria and saprotrophic fungi directly affected the soil microbial functions related to carbon turnover. The biomass of gram-negative bacteria and peroxidase activity were key factors controlling soil carbon dynamics. The interactions between nitrogen addition and plant inputs removal strengthened the correlation between the hydrolases and soil carbon. Conclusions This study showed that nitrogen addition and plant inputs removal could alter soil enzyme activities and further affect soil carbon turnover via microbial regulation. The increase in soil microbial biomass and the microbial regulation of soil carbon both need to be considered when developing effective sustainable forest management practices for northern China. Moreover, further studies are also needed to exactly understand how the complex interaction between the plant and below-ground processes affects the soil microbial community structure.
Wu et al. (2019) Microbial regulation of soil carbon properties under nitrogen addition and plant inputs removal. PeerJ 7:e7343 https://doi.org/10.7717/peerj.7343
Internet addiction and poor quality of life are significantly associated with suicidal ideation of senior high school students in Chongqing, China
Background Adolescence is a vulnerable period of life, and many mental health and behavioral problems emerge during this particular period, including depression, internet addiction (IA), and suicidal behaviors. Poor quality of life (QOL) and IA have been found to be significantly associated with suicidal ideation (SI) among Chinese university students, of whom most have been adults. Nevertheless, their associations with SI are rarely studied among Chinese adolescents. The objective of this study was to examine these relationships in a representative adolescent sample of Chinese senior high school students, who are experiencing an enormous transition from childhood to adulthood. Methods By using multi-stage sampling, a total of 26,688 students were successfully recruited from 29 senior high schools of a very large City in western China, Chongqing municipality. In this cross-sectional online survey, students’ demographic and lifestyle characteristics were collected with a standardized questionnaire. The Young’s IA Test, the Chinese Six-item QOL questionnaire, and item 15 of the Symptom Checklist-90-R were used to measure IA, QOL, and SI, respectively. Results The 1-month prevalence of SI was 11.5% among students of senior high schools in Chongqing, China. Students with SI had significantly higher QOL scores (17.3 ± 3.7 vs. 13.7 ± 3.8, P < 0.001) and higher prevalence of IA (49.6% vs. 25.6%, P < 0.001) than those without SI. After controlling for demographic, lifestyle, and clinical covariates, IA (odd ratio (OR) = 1.15, P = 0.003) and a high QOL score (OR = 1.09, P < 0.001) remained significantly associated with SI. Conclusion Suicidal ideation is prevalent among Chinese adolescents and it is associated with IA and poor QOL. Measures aimed at reducing IA and improving QOL may help prevent suicidal behaviors among Chinese adolescents.
Wang et al. (2019) Internet addiction and poor quality of life are significantly associated with suicidal ideation of senior high school students in Chongqing, China. PeerJ 7:e7357 https://doi.org/10.7717/peerj.7357
Geographic context affects the landscape change and fragmentation caused by wind energy facilities
Wind energy generation affects landscapes as new roads, pads, and transmission lines are constructed. Limiting the landscape change from these facilities likely minimizes impacts to biodiversity and sensitive wildlife species. We examined the effects of wind energy facilities’ geographic context on changes in landscape patterns using three metrics: portion of undeveloped land, core area index, and connectance index. We digitized 39 wind facilities and the surrounding land cover and measured landscape pattern before and after facility construction using the amount, core area, and connectivity of undeveloped land within one km around newly constructed turbines and roads. New facilities decreased the amount of undeveloped land by 1.8% while changes in metrics of landscape pattern ranged from 50 to 140%. Statistical models indicated pre-construction development was a key factor explaining the impact of new wind facilities on landscape metrics, with pre-construction road networks, turbine spacing, and topography having smaller influences. As the proportion of developed land around facilities increased, a higher proportion of the facility utilized pre-construction developed land and a lower density of new roads were built, resulting in smaller impacts to undeveloped landscapes. Building of new road networks was also a predictor of landscape fragmentation. Utilizing existing development and carefully placing turbines may provide opportunities to minimize the impacts of new wind energy facilities.
Spatial and Geographic Information Science
Diffendorfer et al. (2019) Geographic context affects the landscape change and fragmentation caused by wind energy facilities. PeerJ 7:e7129 https://doi.org/10.7717/peerj.7129
Infectious hematopoietic necrosis virus: advances in diagnosis and vaccine development
The aquaculture of salmonid fishes is a multi-billion dollar industry with production over 3 million tons annually. However, infectious hematopoietic necrosis virus (IHNV), which infects and kills salmon and trout, significantly reduces the revenue of the salmon farming industry. Currently, there is no effective treatment for IHNV infected fishes; therefore, early detection and depopulation of the infected fishes remain the most common practices to contain the spread of IHNV. Apart from hygiene practices in aquaculture and isolation of infected fishes, loss of fishes due to IHNV infection can also be significantly reduced through vaccination programs. In the current review, some of the diagnostic methods for IHNV, spanning from clinical diagnosis to cell culture, serological and molecular methods are discussed in detail. In addition, some of the most significant candidate vaccines for IHNV are also extensively discussed, particularly the DNA vaccines.
Yong et al. (2019) Infectious hematopoietic necrosis virus: advances in diagnosis and vaccine development. PeerJ 7:e7151 https://doi.org/10.7717/peerj.7151
Climate change and forest plagues: assessing current and future impacts of diprionid sawflies on the pine forests of north-western Mexico
The imminent threat of climate change lies in its potential to disrupt the balance of ecosystems, particularly vulnerable areas such as mountain-top remnant forests. An example of such a fragile ecosystem is the Sierra San Pedro Mártir (SSPM) National Park of Mexico’s Baja California state, where high levels of endemism can be found, and which is home to one of the country’s few populations of the emblematic Jeffrey pine (Pinus jeffreyi). Recent outbreaks of pine-feeding sawfly larvae in SSPM increase the vulnerability of this forest ecosystem, calling for immediate assessments of the severity of this threat. Here, we present a thorough study of the sawfly’s biology and distribution, carrying out molecular and morphology-based identification of the species and creating model-based predictions of the species distribution in the area. The sawfly was found to belong to an undescribed species of the genus Zadiprion (family Diprionidae) with a one-year life-cycle. The distribution of this species appears to be restricted to the SSPM national park and it will probably persist for at least another 50 years, even considering the effects of climate change.
Aguilera-Molina et al. (2019) Climate change and forest plagues: assessing current and future impacts of diprionid sawflies on the pine forests of north-western Mexico. PeerJ 7:e7220 https://doi.org/10.7717/peerj.7220
Assessing subspecies status of leopards (Panthera pardus) of northern Pakistan using mitochondrial DNA
Despite being classified as critically endangered, little work has been done on leopard protection in Pakistan. Once widely present throughout this region, leopards are now sparsely distributed, and possibly extinct from much of their previously recorded habitat. While leopards show morphological and genetic variation across their species range worldwide, resulting in the classification of nine different subspecies, the leopard genetic structure across Pakistan is unknown, with previous studies including only a very limited sampling. To clarify the genetic status of leopards in Pakistan we investigated the sequence variation in the subunit 5 of the mitochondrial gene NADH from 43 tissue samples and compared it with 238 sequences available from online databases. Phylogenetic analysis clearly separates the Pakistani leopards from the African and Arabian clades, confirming that leopards from Pakistan are members of the Asian clade. Furthermore, we identified two separate subspecies haplotypes within our dataset: P. p. fusca (N = 23) and P. p. saxicolor (N = 12).
Asad et al. (2019) Assessing subspecies status of leopards (Panthera pardus) of northern Pakistan using mitochondrial DNA. PeerJ 7:e7243 https://doi.org/10.7717/peerj.7243
Changes of the erythrocyte phenotype and blood biochemistry in dairy calves during the first ten weeks of age
Background Bovine erythrocytes undergo important changes in their morphology and chemical composition during the first weeks of age, which must be understood to accurately interpret hematology results in calves. The objectives of this prospective cohort study were to describe physiological changes of calf erythrocytes and to investigate mechanisms potentially causing these changes. Methods Blood samples from 30 clinically healthy dairy calves were obtained from birth to the tenth week of age in weekly intervals. Hematological and plasma biochemical parameters as well as the mineral electrolyte content of erythrocytes were determined and followed over time. The changes of parameters characterizing the erythrocyte phenotype over time were compared to the changes of plasma and erythrocyte biochemical parameters and possible associations were investigated using correlation and stepwise regression analyses. Results Although the erythrocyte mean corpuscular volume (MCV) declined from 43.6 ± 3.7 fL to 35.6 ± 3.2 fL between the first and seventh week, the red blood cell count (RBC) increased from 7.2 ± 1.1 × 1012/L to 9.3 ± 1.0 × 1012/L until the fifth week of age. The blood hemoglobin (Hb) concentration increased from 0.96 ± 0.16 g/L to 1.16 ± 0.11 g/L in the first three weeks of age and remained at this level until the end of the study. Changes in MCV were accompanied by a decline of the erythrocyte potassium content (KERY) from 91.9 ± 13.5 to 24.6 ± 7.2 mmol/L and a concomitant increase of the erythrocyte sodium content from 45.0 ± 32.0 to 102.7 ± 26.5 mmol/L. MCV was found to be associated with KERY, the primary determinant of the intra-erythrocyte osmotic pressure from the sixth week of age and with blood hemoglobin, the primary determinant of the intra-erythrocyte oncotic pressure from the eighth week of age, when KERY, blood Hb and MCV already had reached or approached normal levels of adult cattle. The plasma iron concentration was not found to be associated to any of the studied hematological parameters. Conclusion A volume reduction of 20% in bovine neonatal erythrocytes is a physiological change occurring during the first weeks of age and is neither associated with sideropenia nor with anemia in healthy calves. The mechanism driving the observed erythrocyte volume change could not be identified. Results of the correlation and regression analyses indicate that changes in intra-erythrocyte osmotic or oncotic pressure are improbable underlying causes. Results reported here show that KERY is an unreliable indicator for the K homeostasis of the intracellular space in neonatal calves and that a decrease in MCV in early life per-se is an unreliable indicator for the development of microcytic anemia.
Golbeck et al. (2019) Changes of the erythrocyte phenotype and blood biochemistry in dairy calves during the first ten weeks of age. PeerJ 7:e7248 https://doi.org/10.7717/peerj.7248
The relationship between fish abundance and benthic community structure on artificial reefs in the Mid-Atlantic Bight, and the importance of sea whip corals Leptogorgia virgulata
Autogenic engineers (i.e., biogenic structure) add to habitat complexity by altering the environment by their own physical structures. The presence of autogenic engineers is correlated with increases in species abundance and biodiversity. Biogenic structural communities off the coast of Delaware, Maryland, and Virginia (Delmarva) are comprised of multiple species including boring sponge Cliona celata, various hydroids (i.e., Tubularia sp., Obelia sp., Campanular sp.), northern stone coral Astrangia poculata, sea whips Leptogorgia virgulata, and blue mussels Mytilus edulis. Sea whips are soft corals that provide the majority of vertical height to benthic structure off the coast of the Delmarva peninsula. The mid-Atlantic bight is inhabited by several economically valuable fishes; however, data regarding habitat composition, habitat quality, and fish abundance are scarce. We collected quadrat and sea whip images from 12 artificial reef sites (i.e., shipwrecks) ranging from 10 to 24 m depth to determine proportional coverage of biogenic structures and to assess habitat health, respectively. Underwater video surveys were used to estimate fish abundances on the 12 study sites and determine if fish abundance was related to biogenic coverage and habitat health. Our results showed that higher fish abundance was significantly correlated with higher proportional sea whip coral coverage, but showed no significant relationship to other biogenic structure. Assessment of sea whip condition (as a damage index) showed that sea whip corals on artificial reefs off the Delmarva coast exhibited minor signs of degradation that did not differ significantly among study sites.
Schweitzer et al. (2019) The relationship between fish abundance and benthic community structure on artificial reefs in the Mid-Atlantic Bight, and the importance of sea whip corals Leptogorgia virgulata. PeerJ 7:e7277 https://doi.org/10.7717/peerj.7277
Marine biodiversity from zero to a thousand meters at Clipperton Atoll (Île de La Passion), Tropical Eastern Pacific
Clipperton Atoll (Île de La Passion) is the only atoll in the Tropical Eastern Pacific (TEP) ecoregion and, owing to its isolation, possesses several endemic species and is likely an important stepping stone between Oceania, the remainder of the TEP, including other oceanic islands and the west coast of Central America. We describe the biodiversity at this remote atoll from shallow water to depths greater than one thousand meters using a mixture of technologies (SCUBA, stereo baited remote underwater video stations, manned submersible, and deep-sea drop cameras). Seventy-four unique taxa of invertebrates were identified during our expedition. The majority (70%) of these taxa were confined to the top 400 m and consisted mostly of sessile organisms. Decapod crustaceans and black corals (Antipatharia) had the broadest depth ranges, 100–1,497 m and 58–967 m, respectively. Decapods were correlated with the deepest depths, while hard corals were correlated with the shallow depths. There were 96 different fish taxa from 41 families and 15 orders, of which 70% were restricted to depths <200 m. While there was a decreasing trend in richness for both fish and invertebrate taxa with depth, these declines were not linear across the depth gradient. Instead, peaks in richness at ∼200 m and ∼750 m coincided with high turnover due to the appearance of new taxa and disappearance of other taxa within the community and is likely associated with the strong oxygen minimum zone that occurs within the region. The overall depth effect was stronger for fishes compared with invertebrates, which may reflect ecological preferences or differences in taxonomic resolution among groups. The creation of a no-take marine reserve 12 nautical miles around the atoll in 2016 will help conserve this unique and relatively intact ecosystem, which possesses high predator abundance.
Friedlander et al. (2019) Marine biodiversity from zero to a thousand meters at Clipperton Atoll (Île de La Passion), Tropical Eastern Pacific. PeerJ 7:e7279 https://doi.org/10.7717/peerj.7279
UK universities compliance with the Concordat to Support Research Integrity: findings from cross-sectional time-series
Background The Concordat to Support Research Integrity published in 2012 recommends that UK research institutions should provide a named point of contact to receive concerns about research integrity (RI). The Concordat also requires institutions to publish annual RI statements. Objective To see whether contact information for a staff member responsible for RI was readily available from UK university websites and to see how many universities published annual RI statements. Methods UK university websites were searched in mid-2012, mid-2014 and mid-2018. The availability of contact details for RI inquiries, other information about RI and, specifically, an annual RI statement, was recorded. Results The proportion of UK universities publishing an email address for RI inquiries rose from 23% in 2012 (31/134) to 55% in 2018. The same proportion (55%) published at least one annual RI statement in 2018, but only three provided statements for all years from 2012/13. There was great variation in the titles used for the staff member with responsibility for RI which made searching difficult. Conclusion Over 6 years after the publication of the Concordat to Support Research Integrity, nearly half of UK universities are not complying with all its recommendations and do not provide contact details for a staff member with responsibility for RI or an annual statement.
Wager (2019) UK universities compliance with the Concordat to Support Research Integrity: findings from cross-sectional time-series. PeerJ 7:e7292 https://doi.org/10.7717/peerj.7292