PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Body size and temperature effects on standard metabolic rate for determining metabolic scope for activity of the polychaete Hediste (Nereis) diversicolor
items: Egg perivitelline fluid of the invasive snail Pomacea canaliculata affects mice gastrointestinal function and morphology
items: Using accelerometers to develop time-energy budgets of wild fur seals from captive surrogates
items: Size-dependent functional response of Xenopus laevis feeding on mosquito larvae
items: Three, two, one! Revision of the long-bodied sphaerodorids (Sphaerodoridae, Annelida) and synonymization of Ephesiella, Ephesiopsis and Sphaerodorum
items: Evolution of African barbs from the Lake Victoria drainage system, Kenya
items: Spatial analyses of threats to ecosystem service hotspots in Greater Durban, South Africa
items: Inhibitory effect of microalgae and cyanobacteria extracts on influenza virus replication and neuraminidase activity
items: Impact of organic and inorganic fertilizers on the yield and quality of silage corn intercropped with soybean
items: Estimation of antimicrobial activities and fatty acid composition of actinobacteria isolated from water surface of underground lakes from Badzheyskaya and Okhotnichya caves in Siberia

Body size and temperature effects on standard metabolic rate for determining metabolic scope for activity of the polychaete Hediste (Nereis) diversicolor
type: item
type: AcademicArticle
description: Considering the ecological importance and potential value of Hediste diversicolor, a better understanding of its metabolic rate and potential growth rates is required. The aims of this study are: (i) to describe key biometric relationships; (ii) to test the effects of temperature and body size on standard metabolic rate (as measure by oxygen consumption) to determine critical parameters, namely Arrhenius temperature (TA), allometric coefficient (b) and reaction rate; and (iii) to determine the metabolic scope for activity (MSA) of H. diversicolor for further comparison with published specific growth rates. Individuals were collected in a Mediterranean lagoon (France). After 10 days of acclimatization, 7 days at a fixed temperature and 24 h of fasting, resting oxygen consumption rates (VO2) were individually measured in the dark at four different temperatures (11, 17, 22 and 27 °C) in worms weighing from 4 to 94 mgDW (n = 27 per temperature). Results showed that DW and L3 were the most accurate measurements of weight and length, respectively, among all the metrics tested. Conversion of WW (mg), DW (mg) and L3 (mm) were quantified with the following equations: DW = 0.15 × WW, L3 = 0.025 × TL(mm) + 1.44 and DW = 0.8 × L33.68. Using an equation based on temperature and allometric effects, the allometric coefficient (b) was estimated at 0.8 for DW and at 2.83 for L3. The reaction rate (VO2) equaled to 12.33 µmol gDW−1 h−1 and 0.05 µmol mm L3−1 h−1 at the reference temperature (20 °C, 293.15 K). Arrhenius temperature (TA) was 5,707 and 5,664 K (for DW and L3, respectively). Metabolic scope for activity ranged from 120.1 to 627.6 J gDW−1 d−1. Predicted maximum growth rate increased with temperature, with expected values of 7–10% in the range of 15–20 °C. MSA was then used to evaluate specific growth rates (SGR) in several experiments. This paper may be used as a reference and could have interesting applications in the fields of aquaculture, ecology and biogeochemical proce…
format: application/pdf
format: text/html
creator: Helena Lopes Galasso
creator: Marion Richard
creator: Sébastien Lefebvre
creator: Catherine Aliaume
creator: Myriam D. Callier
subject: Aquaculture, Fisheries and Fish Science
subject: Marine Biology
description: doi:10.7717/peerj.5675
publisher: PeerJ Inc.
rights: © 2018 Galasso et al.
abstract: Considering the ecological importance and potential value of Hediste diversicolor, a better understanding of its metabolic rate and potential growth rates is required. The aims of this study are: (i) to describe key biometric relationships; (ii) to test the effects of temperature and body size on standard metabolic rate (as measure by oxygen consumption) to determine critical parameters, namely Arrhenius temperature (TA), allometric coefficient (b) and reaction rate; and (iii) to determine the metabolic scope for activity (MSA) of H. diversicolor for further comparison with published specific growth rates. Individuals were collected in a Mediterranean lagoon (France). After 10 days of acclimatization, 7 days at a fixed temperature and 24 h of fasting, resting oxygen consumption rates (VO2) were individually measured in the dark at four different temperatures (11, 17, 22 and 27 °C) in worms weighing from 4 to 94 mgDW (n = 27 per temperature). Results showed that DW and L3 were the most accurate measurements of weight and length, respectively, among all the metrics tested. Conversion of WW (mg), DW (mg) and L3 (mm) were quantified with the following equations: DW = 0.15 × WW, L3 = 0.025 × TL(mm) + 1.44 and DW = 0.8 × L33.68. Using an equation based on temperature and allometric effects, the allometric coefficient (b) was estimated at 0.8 for DW and at 2.83 for L3. The reaction rate (VO2) equaled to 12.33 µmol gDW−1 h−1 and 0.05 µmol mm L3−1 h−1 at the reference temperature (20 °C, 293.15 K). Arrhenius temperature (TA) was 5,707 and 5,664 K (for DW and L3, respectively). Metabolic scope for activity ranged from 120.1 to 627.6 J gDW−1 d−1. Predicted maximum growth rate increased with temperature, with expected values of 7–10% in the range of 15–20 °C. MSA was then used to evaluate specific growth rates (SGR) in several experiments. This paper may be used as a reference and could have interesting applications in the fields of aquaculture, ecology and biogeochemical proce…
bibliographic citation: Galasso et al. (2018) Body size and temperature effects on standard metabolic rate for determining metabolic scope for activity of the polychaete Hediste (Nereis) diversicolor. PeerJ 6:e5675 https://doi.org/10.7717/peerj.5675
date submitted: 2017-11-29
date accepted: 2018-08-30
issued: 2018-10-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Galasso
  given name: Helena Lopes
author list: Agent
  family name: Richard
  given name: Marion
author list: Agent
  family name: Lefebvre
  given name: Sébastien
author list: Agent
  family name: Aliaume
  given name: Catherine
author list: Agent
  family name: Callier
  given name: Myriam D.
doi: 10.7717/peerj.5675
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-29
copyright: ©2018 Galasso et al.
attribution name: Galasso et al.

Egg perivitelline fluid of the invasive snail Pomacea canaliculata affects mice gastrointestinal function and morphology
type: item
type: AcademicArticle
description: Background Species beloging to the genus Pomacea (Ampullariidae), often referred as apple snails, are freshwater, amphibious snails native to South, Central and North America. Some species such as P. canaliculata have become a driver of ecosystem changes in wetlands and an important rice and taro pest after its introduction to Asia and other parts of the world. Females deposit colored egg clutches above the waterline, a reproductive strategy that exposes the eggs to harsh conditions and terrestrial predation. However, eggs have no reported predators in their native range, probably because of the acquisition of unparalleled biochemical defenses provided by a set of proteins (perivitellins) that nourish embryos and protect them from predators and abiotic factors. Notably, ingestion of egg perivitelline fluid (PVF) decreases rat growth rate and alters their gastrointestinal morphology. The aim of the study is to determine the effect of apple snail egg PVF on mice gut digestive activity, morphology and nutrient absorption. Methods Carbohydrate digestion by intestinal disaccharidases (sucrase-isomaltase and maltase-glucoamylase) was evaluated ex vivo in mice gavaged with 1 or 4 doses of PVF. Changes in gut morphological and absorptive surface were measured. In addition, alteration on nutrient absorption rates, transport pathways and intestinal permeability was evaluated by luminal perfusions of small intestine with radiolabeled L-proline (absorbed by paracellular and transcellular pathways) and L-arabinose (absorbed exclusively by paracellular pathway). Results Perivitelline fluid affected mice displayed significant morphological changes in the small intestine epithelium inducing the appearance of shorter and wider villi as well as fused villi. This resulted in a diminished absorptive surface, notably in the proximal portion. Likewise, the activity of disaccharidases diminished in the proximal portion of the intestine. Total absorption of L-proline increased in treated m…
format: application/pdf
format: text/html
creator: Matías Giglio
creator: Cintia Garro
creator: Enrique Caviedes-Vidal
creator: Horacio Heras
subject: Zoology
subject: Histology
subject: Freshwater Biology
description: doi:10.7717/peerj.5314
publisher: PeerJ Inc.
rights: © 2018 Giglio et al.
abstract: Background Species beloging to the genus Pomacea (Ampullariidae), often referred as apple snails, are freshwater, amphibious snails native to South, Central and North America. Some species such as P. canaliculata have become a driver of ecosystem changes in wetlands and an important rice and taro pest after its introduction to Asia and other parts of the world. Females deposit colored egg clutches above the waterline, a reproductive strategy that exposes the eggs to harsh conditions and terrestrial predation. However, eggs have no reported predators in their native range, probably because of the acquisition of unparalleled biochemical defenses provided by a set of proteins (perivitellins) that nourish embryos and protect them from predators and abiotic factors. Notably, ingestion of egg perivitelline fluid (PVF) decreases rat growth rate and alters their gastrointestinal morphology. The aim of the study is to determine the effect of apple snail egg PVF on mice gut digestive activity, morphology and nutrient absorption. Methods Carbohydrate digestion by intestinal disaccharidases (sucrase-isomaltase and maltase-glucoamylase) was evaluated ex vivo in mice gavaged with 1 or 4 doses of PVF. Changes in gut morphological and absorptive surface were measured. In addition, alteration on nutrient absorption rates, transport pathways and intestinal permeability was evaluated by luminal perfusions of small intestine with radiolabeled L-proline (absorbed by paracellular and transcellular pathways) and L-arabinose (absorbed exclusively by paracellular pathway). Results Perivitelline fluid affected mice displayed significant morphological changes in the small intestine epithelium inducing the appearance of shorter and wider villi as well as fused villi. This resulted in a diminished absorptive surface, notably in the proximal portion. Likewise, the activity of disaccharidases diminished in the proximal portion of the intestine. Total absorption of L-proline increased in treated m…
bibliographic citation: Giglio et al. (2018) Egg perivitelline fluid of the invasive snail Pomacea canaliculata affects mice gastrointestinal function and morphology. PeerJ 6:e5314 https://doi.org/10.7717/peerj.5314
date submitted: 2018-03-28
date accepted: 2018-07-05
issued: 2018-10-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Giglio
  given name: Matías
author list: Agent
  family name: Garro
  given name: Cintia
author list: Agent
  family name: Caviedes-Vidal
  given name: Enrique
author list: Agent
  family name: Heras
  given name: Horacio
doi: 10.7717/peerj.5314
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-29
copyright: ©2018 Giglio et al.
attribution name: Giglio et al.

Using accelerometers to develop time-energy budgets of wild fur seals from captive surrogates
type: item
type: AcademicArticle
description: Background Accurate time-energy budgets summarise an animal’s energy expenditure in a given environment, and are potentially a sensitive indicator of how an animal responds to changing resources. Deriving accurate time-energy budgets requires an estimate of time spent in different activities and of the energetic cost of that activity. Bio-loggers (e.g., accelerometers) may provide a solution for monitoring animals such as fur seals that make long-duration foraging trips. Using low resolution to record behaviour may aid in the transmission of data, negating the need to recover the device. Methods This study used controlled captive experiments and previous energetic research to derive time-energy budgets of juvenile Australian fur seals (Arctocephalus pusillus) equipped with tri-axial accelerometers. First, captive fur seals and sea lions were equipped with accelerometers recording at high (20 Hz) and low (1 Hz) resolutions, and their behaviour recorded. Using this data, machine learning models were trained to recognise four states—foraging, grooming, travelling and resting. Next, the energetic cost of each behaviour, as a function of location (land or water), season and digestive state (pre- or post-prandial) was estimated. Then, diving and movement data were collected from nine wild juvenile fur seals wearing accelerometers recording at high- and low- resolutions. Models developed from captive seals were applied to accelerometry data from wild juvenile Australian fur seals and, finally, their time-energy budgets were reconstructed. Results Behaviour classification models built with low resolution (1 Hz) data correctly classified captive seal behaviours with very high accuracy (up to 90%) and recorded without interruption. Therefore, time-energy budgets of wild fur seals were constructed with these data. The reconstructed time-energy budgets revealed that juvenile fur seals expended the same amount of energy as adults of similar species. No significant differences in…
format: application/pdf
format: text/html
creator: Monique A. Ladds
creator: Marcus Salton
creator: David P. Hocking
creator: Rebecca R. McIntosh
creator: Adam P. Thompson
creator: David J. Slip
creator: Robert G. Harcourt
subject: Animal Behavior
subject: Ecology
subject: Marine Biology
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.5814
publisher: PeerJ Inc.
rights: © 2018 Ladds et al.
abstract: Background Accurate time-energy budgets summarise an animal’s energy expenditure in a given environment, and are potentially a sensitive indicator of how an animal responds to changing resources. Deriving accurate time-energy budgets requires an estimate of time spent in different activities and of the energetic cost of that activity. Bio-loggers (e.g., accelerometers) may provide a solution for monitoring animals such as fur seals that make long-duration foraging trips. Using low resolution to record behaviour may aid in the transmission of data, negating the need to recover the device. Methods This study used controlled captive experiments and previous energetic research to derive time-energy budgets of juvenile Australian fur seals (Arctocephalus pusillus) equipped with tri-axial accelerometers. First, captive fur seals and sea lions were equipped with accelerometers recording at high (20 Hz) and low (1 Hz) resolutions, and their behaviour recorded. Using this data, machine learning models were trained to recognise four states—foraging, grooming, travelling and resting. Next, the energetic cost of each behaviour, as a function of location (land or water), season and digestive state (pre- or post-prandial) was estimated. Then, diving and movement data were collected from nine wild juvenile fur seals wearing accelerometers recording at high- and low- resolutions. Models developed from captive seals were applied to accelerometry data from wild juvenile Australian fur seals and, finally, their time-energy budgets were reconstructed. Results Behaviour classification models built with low resolution (1 Hz) data correctly classified captive seal behaviours with very high accuracy (up to 90%) and recorded without interruption. Therefore, time-energy budgets of wild fur seals were constructed with these data. The reconstructed time-energy budgets revealed that juvenile fur seals expended the same amount of energy as adults of similar species. No significant differences in…
bibliographic citation: Ladds et al. (2018) Using accelerometers to develop time-energy budgets of wild fur seals from captive surrogates. PeerJ 6:e5814 https://doi.org/10.7717/peerj.5814
date submitted: 2018-02-22
date accepted: 2018-09-22
issued: 2018-10-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ladds
  given name: Monique A.
author list: Agent
  family name: Salton
  given name: Marcus
author list: Agent
  family name: Hocking
  given name: David P.
author list: Agent
  family name: McIntosh
  given name: Rebecca R.
author list: Agent
  family name: Thompson
  given name: Adam P.
author list: Agent
  family name: Slip
  given name: David J.
author list: Agent
  family name: Harcourt
  given name: Robert G.
doi: 10.7717/peerj.5814
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-26
copyright: ©2018 Ladds et al.
attribution name: Ladds et al.

Size-dependent functional response of Xenopus laevis feeding on mosquito larvae
type: item
type: AcademicArticle
description: Predators can play an important role in regulating prey abundance and diversity, determining food web structure and function, and contributing to important ecosystem services, including the regulation of agricultural pests and disease vectors. Thus, the ability to predict predator impact on prey is an important goal in ecology. Often, predators of the same species are assumed to be functionally equivalent, despite considerable individual variation in predator traits known to be important for shaping predator–prey interactions, like body size. This assumption may greatly oversimplify our understanding of within-species functional diversity and undermine our ability to predict predator effects on prey. Here, we examine the degree to which predator–prey interactions are functionally homogenous across a natural range of predator body sizes. Specifically, we quantify the size-dependence of the functional response of African clawed frogs (Xenopus laevis) preying on mosquito larvae (Culex pipiens). Three size classes of predators, small (15–30 mm snout-vent length), medium (50–60 mm) and large (105–120 mm), were presented with five densities of prey to determine functional response type and to estimate search efficiency and handling time parameters generated from the models. The results of mesocosm experiments showed that type of functional response of X. laevis changed with size: small predators exhibited a Type II response, while medium and large predators exhibited Type III responses. Functional response data showed an inversely proportional relationship between predator attack rate and predator size. Small and medium predators had highest and lowest handling time, respectively. The change in functional response with the size of predator suggests that predators with overlapping cohorts may have a dynamic impact on prey populations. Therefore, predicting the functional response of a single size-matched predator in an experiment may misrepresent the predator’s potential i…
format: application/pdf
format: text/html
creator: Corey J. Thorp
creator: Mhairi E. Alexander
creator: James R. Vonesh
creator: John Measey
subject: Animal Behavior
subject: Ecology
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.5813
publisher: PeerJ Inc.
rights: © 2018 Thorp et al.
abstract: Predators can play an important role in regulating prey abundance and diversity, determining food web structure and function, and contributing to important ecosystem services, including the regulation of agricultural pests and disease vectors. Thus, the ability to predict predator impact on prey is an important goal in ecology. Often, predators of the same species are assumed to be functionally equivalent, despite considerable individual variation in predator traits known to be important for shaping predator–prey interactions, like body size. This assumption may greatly oversimplify our understanding of within-species functional diversity and undermine our ability to predict predator effects on prey. Here, we examine the degree to which predator–prey interactions are functionally homogenous across a natural range of predator body sizes. Specifically, we quantify the size-dependence of the functional response of African clawed frogs (Xenopus laevis) preying on mosquito larvae (Culex pipiens). Three size classes of predators, small (15–30 mm snout-vent length), medium (50–60 mm) and large (105–120 mm), were presented with five densities of prey to determine functional response type and to estimate search efficiency and handling time parameters generated from the models. The results of mesocosm experiments showed that type of functional response of X. laevis changed with size: small predators exhibited a Type II response, while medium and large predators exhibited Type III responses. Functional response data showed an inversely proportional relationship between predator attack rate and predator size. Small and medium predators had highest and lowest handling time, respectively. The change in functional response with the size of predator suggests that predators with overlapping cohorts may have a dynamic impact on prey populations. Therefore, predicting the functional response of a single size-matched predator in an experiment may misrepresent the predator’s potential i…
bibliographic citation: Thorp et al. (2018) Size-dependent functional response of Xenopus laevis feeding on mosquito larvae. PeerJ 6:e5813 https://doi.org/10.7717/peerj.5813
date submitted: 2018-02-20
date accepted: 2018-09-21
issued: 2018-10-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Thorp
  given name: Corey J.
author list: Agent
  family name: Alexander
  given name: Mhairi E.
author list: Agent
  family name: Vonesh
  given name: James R.
author list: Agent
  family name: Measey
  given name: John
doi: 10.7717/peerj.5813
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-26
copyright: ©2018 Thorp et al.
attribution name: Thorp et al.

Three, two, one! Revision of the long-bodied sphaerodorids (Sphaerodoridae, Annelida) and synonymization of Ephesiella, Ephesiopsis and Sphaerodorum
type: item
type: AcademicArticle
description: Background Long-bodied sphaerodorids (Annelida, Sphaerodoridae) is the common name for members of the three closely and morphologically homogenous currently accepted genera of benthic marine bristle worms: Ephesiella, Ephesiopsis and Sphaerodorum. Members of this group share the presence of two dorsal and longitudinal rows of macrotubercles with terminal papillae, and two longitudinal rows of microtubercles, features that are unique among sphaerodorids. Genera are distinguished by the chaetae morphology. Members of Ephesiella are characterised by having compound chaetae (except, sometimes, simple chaetae in the first chaetigers), Sphaerodorum bear only simple chaetae, and Ephesiopsis have both compound and simple chaetae in all parapodia. Methods Mitochondrial (partial COI and 16S rDNA) and nuclear (partial 18S rDNA and 28S rDNA) sequence data of long-bodied sphaerodorids with compound and simple chaetae, and an outgroup of additional seven sphaerodorid species were analysed separately and in combination using Bayesian inference (BA), and Maximum Likelihood (ML) methods. Long-bodied sphaerodorids from around the world (including type specimens) were examined under a range of optical equipment in order to evaluate putative generic and specific diagnostic features, in addition to intraspecific variability. Results Phylogenetic analyses of mitochondrial and nuclear DNA sequences of specimens identified as Ephesiella and Sphaerodorum, based on chaeta morphology, were performed. Sphaerodorum and Ephesiella were recovered as paraphyletic and nested within each other. Revision of current nominal species diagnostic features are performed and discussed. Discussion Results contradict current generic definitions. Recovery of paraphyletic compound and simple chaetae clades urge the synonymization of these two genera of long-bodied sphaerodorids. Morphological data also suggest the synonymization of Ephesiopsis.
format: application/pdf
format: text/html
creator: María Capa
creator: Torkild Bakken
creator: Karin Meißner
creator: Arne Nygren
subject: Biodiversity
subject: Evolutionary Studies
subject: Genetics
subject: Marine Biology
subject: Taxonomy
description: doi:10.7717/peerj.5783
publisher: PeerJ Inc.
rights: © 2018 Capa et al.
abstract: Background Long-bodied sphaerodorids (Annelida, Sphaerodoridae) is the common name for members of the three closely and morphologically homogenous currently accepted genera of benthic marine bristle worms: Ephesiella, Ephesiopsis and Sphaerodorum. Members of this group share the presence of two dorsal and longitudinal rows of macrotubercles with terminal papillae, and two longitudinal rows of microtubercles, features that are unique among sphaerodorids. Genera are distinguished by the chaetae morphology. Members of Ephesiella are characterised by having compound chaetae (except, sometimes, simple chaetae in the first chaetigers), Sphaerodorum bear only simple chaetae, and Ephesiopsis have both compound and simple chaetae in all parapodia. Methods Mitochondrial (partial COI and 16S rDNA) and nuclear (partial 18S rDNA and 28S rDNA) sequence data of long-bodied sphaerodorids with compound and simple chaetae, and an outgroup of additional seven sphaerodorid species were analysed separately and in combination using Bayesian inference (BA), and Maximum Likelihood (ML) methods. Long-bodied sphaerodorids from around the world (including type specimens) were examined under a range of optical equipment in order to evaluate putative generic and specific diagnostic features, in addition to intraspecific variability. Results Phylogenetic analyses of mitochondrial and nuclear DNA sequences of specimens identified as Ephesiella and Sphaerodorum, based on chaeta morphology, were performed. Sphaerodorum and Ephesiella were recovered as paraphyletic and nested within each other. Revision of current nominal species diagnostic features are performed and discussed. Discussion Results contradict current generic definitions. Recovery of paraphyletic compound and simple chaetae clades urge the synonymization of these two genera of long-bodied sphaerodorids. Morphological data also suggest the synonymization of Ephesiopsis.
bibliographic citation: Capa et al. (2018) Three, two, one! Revision of the long-bodied sphaerodorids (Sphaerodoridae, Annelida) and synonymization of Ephesiella, Ephesiopsis and Sphaerodorum. PeerJ 6:e5783 https://doi.org/10.7717/peerj.5783
date submitted: 2018-07-06
date accepted: 2018-09-18
issued: 2018-10-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Capa
  given name: María
author list: Agent
  family name: Bakken
  given name: Torkild
author list: Agent
  family name: Meißner
  given name: Karin
author list: Agent
  family name: Nygren
  given name: Arne
doi: 10.7717/peerj.5783
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-26
copyright: ©2018 Capa et al.
attribution name: Capa et al.

Evolution of African barbs from the Lake Victoria drainage system, Kenya
type: item
type: AcademicArticle
description: The Lake Victoria drainage basin (LVD) in Kenya is home to ten nominal species of small barbs (Enteromius) and one of large barbs (Labeobarbus altianalis). A recent molecular study genetically characterized small barbs in this region and found evidence of introgression between certain species, complicating the taxonomy and species identification of these fishes. This study aimed to extend our understanding on the evolution of these fishes by: (1) determining whether putatively pure individuals of Enteromius cercops are found in the Kenyan LVD, as the previous study only found hybrid individuals of this species in this region; (2) testing the sister relationship between Enteromius profundus, endemic to Lake Victoria, and Enteromius radiatus, also found in Lake Victoria, which had been previously synonymized; (3) examining the phylogenetic relationships of small barbs of the Kenyan LVD with those reported from other ichthyological provinces of Africa; and (4) examining the phylogenetic relationships of Labeobarbus altianalis with other Labeobarbus species. To this end, we obtained mitochondrial Cytochrome b and nuclear Growth Hormone (GH) intron 2 gene sequences of nine Enteromius species from the LVD in Kenya, as well as cytochrome b sequences for L. altianalis. We conducted Maximum likelihood and Bayesian phylogenetic analyses to establish their evolutionary relationships in relation to many other barbs specimens from Africa. Phylogenetic analyses did not reveal instances of hybridization/introgression among the individuals sequenced by us. A sister relationship between E. profundus and E. radiatus was not found. This latter species shows instead a sister relationship with a lineage comprised of two species from West Africa. Other sister relationships between taxa from the East coast and other ecoregions from Africa are observed, suggesting that past drainage connections and vicariant events contributed to the diversification of Enteromius. Finally, only a single ha…
format: application/pdf
format: text/html
creator: Violet M. Ndeda
creator: Mariana Mateos
creator: Luis A. Hurtado
subject: Biodiversity
subject: Evolutionary Studies
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.5762
publisher: PeerJ Inc.
rights: © 2018 Ndeda et al.
abstract: The Lake Victoria drainage basin (LVD) in Kenya is home to ten nominal species of small barbs (Enteromius) and one of large barbs (Labeobarbus altianalis). A recent molecular study genetically characterized small barbs in this region and found evidence of introgression between certain species, complicating the taxonomy and species identification of these fishes. This study aimed to extend our understanding on the evolution of these fishes by: (1) determining whether putatively pure individuals of Enteromius cercops are found in the Kenyan LVD, as the previous study only found hybrid individuals of this species in this region; (2) testing the sister relationship between Enteromius profundus, endemic to Lake Victoria, and Enteromius radiatus, also found in Lake Victoria, which had been previously synonymized; (3) examining the phylogenetic relationships of small barbs of the Kenyan LVD with those reported from other ichthyological provinces of Africa; and (4) examining the phylogenetic relationships of Labeobarbus altianalis with other Labeobarbus species. To this end, we obtained mitochondrial Cytochrome b and nuclear Growth Hormone (GH) intron 2 gene sequences of nine Enteromius species from the LVD in Kenya, as well as cytochrome b sequences for L. altianalis. We conducted Maximum likelihood and Bayesian phylogenetic analyses to establish their evolutionary relationships in relation to many other barbs specimens from Africa. Phylogenetic analyses did not reveal instances of hybridization/introgression among the individuals sequenced by us. A sister relationship between E. profundus and E. radiatus was not found. This latter species shows instead a sister relationship with a lineage comprised of two species from West Africa. Other sister relationships between taxa from the East coast and other ecoregions from Africa are observed, suggesting that past drainage connections and vicariant events contributed to the diversification of Enteromius. Finally, only a single ha…
bibliographic citation: Ndeda et al. (2018) Evolution of African barbs from the Lake Victoria drainage system, Kenya. PeerJ 6:e5762 https://doi.org/10.7717/peerj.5762
date submitted: 2018-06-26
date accepted: 2018-09-16
issued: 2018-10-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ndeda
  given name: Violet M.
author list: Agent
  family name: Mateos
  given name: Mariana
author list: Agent
  family name: Hurtado
  given name: Luis A.
doi: 10.7717/peerj.5762
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-26
copyright: ©2018 Ndeda et al.
attribution name: Ndeda et al.

Spatial analyses of threats to ecosystem service hotspots in Greater Durban, South Africa
type: item
type: AcademicArticle
description: Background Population growth at all scales and rapid rates of urbanization, particularly in the global South, are placing increasing pressure on ecosystems and their ability to provide services essential for human well-being. The spatial consideration of threats to ecosystem services related to changes in land use is necessary in order to avoid undue impacts on society due to the loss or reduced supply of ecosystem services. This study assesses the potential threats of land use change from strategic and local development proposals to ecosystem services in the city of Durban. Methods We analysed the spatial relationship between five categories of ecosystem service hotspots (carbon storage, water yield, sediment retention, nutrient retention and flood attenuation) and urban land use change related to selected strategic planning proposals, development proposals and sand-mining applications in Durban, South Africa (eThekwini Municipality) with a view to determining the consequences for progress towards a more sustainable development path in the city. We identified the potential levels of threat related to habitat destruction or transformation for the five categories of ecosystem services and a subset of 13 ecosystem service hotspots, using GIS spatial analysis tools. Results The results show that on average, should Durban’s strategic development plans be realised, approximately 42% loss of ecosystem service hotspots is expected in the two municipal town-planning regions assessed. With respect to development applications between 2009 and 2012, approximately 36% of all environmental impact assessments and 84% of sand mining applications occurred within ecosystem service hotspots within Durban. Discussion The findings highlight the tension between short-term development pressures and longer-term sustainability goals and confirm that current planning and development proposals pose a threat to ecosystems and their ability to deliver services that support human well-being in …
format: application/pdf
format: text/html
creator: Rashieda Davids
creator: Mathieu Rouget
creator: Richard Boon
creator: Debra Roberts
subject: Ecosystem Science
subject: Coupled Natural and Human Systems
subject: Natural Resource Management
subject: Environmental Impacts
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.5723
publisher: PeerJ Inc.
rights: © 2018 Davids et al.
abstract: Background Population growth at all scales and rapid rates of urbanization, particularly in the global South, are placing increasing pressure on ecosystems and their ability to provide services essential for human well-being. The spatial consideration of threats to ecosystem services related to changes in land use is necessary in order to avoid undue impacts on society due to the loss or reduced supply of ecosystem services. This study assesses the potential threats of land use change from strategic and local development proposals to ecosystem services in the city of Durban. Methods We analysed the spatial relationship between five categories of ecosystem service hotspots (carbon storage, water yield, sediment retention, nutrient retention and flood attenuation) and urban land use change related to selected strategic planning proposals, development proposals and sand-mining applications in Durban, South Africa (eThekwini Municipality) with a view to determining the consequences for progress towards a more sustainable development path in the city. We identified the potential levels of threat related to habitat destruction or transformation for the five categories of ecosystem services and a subset of 13 ecosystem service hotspots, using GIS spatial analysis tools. Results The results show that on average, should Durban’s strategic development plans be realised, approximately 42% loss of ecosystem service hotspots is expected in the two municipal town-planning regions assessed. With respect to development applications between 2009 and 2012, approximately 36% of all environmental impact assessments and 84% of sand mining applications occurred within ecosystem service hotspots within Durban. Discussion The findings highlight the tension between short-term development pressures and longer-term sustainability goals and confirm that current planning and development proposals pose a threat to ecosystems and their ability to deliver services that support human well-being in …
bibliographic citation: Davids et al. (2018) Spatial analyses of threats to ecosystem service hotspots in Greater Durban, South Africa. PeerJ 6:e5723 https://doi.org/10.7717/peerj.5723
date submitted: 2018-02-12
date accepted: 2018-09-11
issued: 2018-10-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Davids
  given name: Rashieda
author list: Agent
  family name: Rouget
  given name: Mathieu
author list: Agent
  family name: Boon
  given name: Richard
author list: Agent
  family name: Roberts
  given name: Debra
doi: 10.7717/peerj.5723
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-26
copyright: ©2018 Davids et al.
attribution name: Davids et al.

Inhibitory effect of microalgae and cyanobacteria extracts on influenza virus replication and neuraminidase activity
type: item
type: AcademicArticle
description: Background The influenza virus can cause seasonal infections with mild to severe symptoms, circulating worldwide, and it can affect people in any age group. Therefore, this infection is a serious public health problem that causes severe illness and death in high-risk populations. Every year, 0.5% of the world’s population is infected by this pathogen. This percentage can increase up to ten times during pandemics. Influenza vaccination is the most effective way to prevent disease. In addition, anti-influenza drugs are essential for prophylactic and therapeutic interventions. The oseltamivir (OST, a neuraminidase inhibitor) is the primary antiviral used in clinics during outbreaks. However, OST resistant viruses may emerge naturally or due to antiviral pressure, with a prevalence of 1–2% worldwide. Thus, the search for new anti-influenza drugs is extremely important. Currently, several groups have been developing studies describing the biotechnological potential of microalgae and cyanobacteria, including antiviral activity of their extracts. In Brazil, this potential is poorly known and explored. Methods With the aim of increasing the knowledge on this topic, 38 extracts from microalgae and cyanobacteria isolated from marine and freshwater biomes in Brazil were tested against: cellular toxicity; OST-sensitive and resistant influenza replications; and neuraminidase activity. Results For this purpose, Madin-Darby Canine Kidney (MDCK)-infected cells were treated with 200 μg/mL of each extract. A total of 17 extracts (45%) inhibited influenza A replication, with seven of them resulting in more than 80% inhibition. Moreover, functional assays performed with viral neuraminidase revealed two extracts (from Leptolyngbya sp. and Chlorellaceae) with IC50 mean < 210 μg/mL for influenza A and B, and also OST-sensitive and resistant strains. Furthermore, MDCK cells exposed to 1 mg/mL of all the extracts showed viability higher than 80%. Discussion Our results suggest that extracts…
format: application/pdf
format: text/html
creator: Thauane Silva
creator: Paulo S. Salomon
creator: Lidilhone Hamerski
creator: Juline Walter
creator: Rafael B. Menezes
creator: José Edson Siqueira
creator: Aline Santos
creator: Jéssica Aparecida Morais Santos
creator: Natália Ferme
creator: Thaise Guimarães
creator: Giovana O. Fistarol
creator: Paulo I. Hargreaves
creator: Cristiane Thompson
creator: Fabiano Thompson
creator: Thiago Moreno Souza
creator: Marilda Siqueira
creator: Milene Miranda
subject: Marine Biology
subject: Virology
subject: Freshwater Biology
description: doi:10.7717/peerj.5716
publisher: PeerJ Inc.
rights: © 2018 Silva et al.
abstract: Background The influenza virus can cause seasonal infections with mild to severe symptoms, circulating worldwide, and it can affect people in any age group. Therefore, this infection is a serious public health problem that causes severe illness and death in high-risk populations. Every year, 0.5% of the world’s population is infected by this pathogen. This percentage can increase up to ten times during pandemics. Influenza vaccination is the most effective way to prevent disease. In addition, anti-influenza drugs are essential for prophylactic and therapeutic interventions. The oseltamivir (OST, a neuraminidase inhibitor) is the primary antiviral used in clinics during outbreaks. However, OST resistant viruses may emerge naturally or due to antiviral pressure, with a prevalence of 1–2% worldwide. Thus, the search for new anti-influenza drugs is extremely important. Currently, several groups have been developing studies describing the biotechnological potential of microalgae and cyanobacteria, including antiviral activity of their extracts. In Brazil, this potential is poorly known and explored. Methods With the aim of increasing the knowledge on this topic, 38 extracts from microalgae and cyanobacteria isolated from marine and freshwater biomes in Brazil were tested against: cellular toxicity; OST-sensitive and resistant influenza replications; and neuraminidase activity. Results For this purpose, Madin-Darby Canine Kidney (MDCK)-infected cells were treated with 200 μg/mL of each extract. A total of 17 extracts (45%) inhibited influenza A replication, with seven of them resulting in more than 80% inhibition. Moreover, functional assays performed with viral neuraminidase revealed two extracts (from Leptolyngbya sp. and Chlorellaceae) with IC50 mean < 210 μg/mL for influenza A and B, and also OST-sensitive and resistant strains. Furthermore, MDCK cells exposed to 1 mg/mL of all the extracts showed viability higher than 80%. Discussion Our results suggest that extracts…
bibliographic citation: Silva et al. (2018) Inhibitory effect of microalgae and cyanobacteria extracts on influenza virus replication and neuraminidase activity. PeerJ 6:e5716 https://doi.org/10.7717/peerj.5716
date submitted: 2018-04-23
date accepted: 2018-09-10
issued: 2018-10-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Silva
  given name: Thauane
author list: Agent
  family name: S. Salomon
  given name: Paulo
author list: Agent
  family name: Hamerski
  given name: Lidilhone
author list: Agent
  family name: Walter
  given name: Juline
author list: Agent
  family name: B. Menezes
  given name: Rafael
author list: Agent
  family name: Siqueira
  given name: José Edson
author list: Agent
  family name: Santos
  given name: Aline
author list: Agent
  family name: Santos
  given name: Jéssica Aparecida Morais
author list: Agent
  family name: Ferme
  given name: Natália
author list: Agent
  family name: Guimarães
  given name: Thaise
author list: Agent
  family name: O. Fistarol
  given name: Giovana
author list: Agent
  family name: I. Hargreaves
  given name: Paulo
author list: Agent
  family name: Thompson
  given name: Cristiane
author list: Agent
  family name: Thompson
  given name: Fabiano
author list: Agent
  family name: Souza
  given name: Thiago Moreno
author list: Agent
  family name: Siqueira
  given name: Marilda
author list: Agent
  family name: Miranda
  given name: Milene
doi: 10.7717/peerj.5716
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-26
copyright: ©2018 Silva et al.
attribution name: Silva et al.

Impact of organic and inorganic fertilizers on the yield and quality of silage corn intercropped with soybean
type: item
type: AcademicArticle
description: Background Corn silage is an important feed for intense ruminant production, but the growth of corn relies heavily on the use of chemical fertilizers. Sustainable crop production requires careful management of all nutrient sources available on a farm, particularly in corn-based cropping systems. Methods Experiments were conducted to determine the appropriate technique of corn-legume intercropping in conjunction with the supplemental use of chemical fertilizers, organic manure, and biofertilizers (BFs). Acetylene reduction assays (ARAs) were also performed on corn and soybean roots. Results Combining chemical fertilizers with chicken manure (CM) in a 50:50 ratio and applying 50% NPK+50% CM+BF produced fresh forage and dry matter (DM) yields that were similar to those produced in the 100% nitrogen (N), phosphorus (P), potassium (K) treatment. Among the lone fertilizer treatments, the inorganic fertilizer (100% NPK) treatment produced the highest DM yield (13.86 t/ha) of forage and outyielded the 100% CM (9.74 t/ha) treatment. However, when CM was combined with NPK, the resulting DM yield of forage (13.86 t/ha) was the same as that resulting from 100% NPK (13.68 t/ha). Compared with CM applications alone, combinations of NPK and CM applications resulted in increased plant height, crop growth rates (CGRs) and leaf area index (LAI), but the values of these parameters were similar to those resulting from 100% NPK application. Fertilizers in which the ratio was 50% CM+50% NPK or 50% CM+50% NPK+BF resulted in protein yields that were similar to those resulting from conventional fertilizers. Similarly, the CP content did not significantly differ between applications of the 100% NPK and 50% CM+50% NPK fertilizers. The use of BFs had no significant impact on improving either the yield or quality of forage fertilized with inorganic or organic fertilizer. Lactic acid responded differently to different fertilizer applications and was significantly higher in the fertilized plots t…
format: application/pdf
format: text/html
creator: Ali Baghdadi
creator: Ridzwan A. Halim
creator: Ali Ghasemzadeh
creator: Mohd Fauzi Ramlan
creator: Siti Zaharah Sakimin
subject: Agricultural Science
subject: Ecology
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.5280
publisher: PeerJ Inc.
rights: © 2018 Baghdadi et al.
abstract: Background Corn silage is an important feed for intense ruminant production, but the growth of corn relies heavily on the use of chemical fertilizers. Sustainable crop production requires careful management of all nutrient sources available on a farm, particularly in corn-based cropping systems. Methods Experiments were conducted to determine the appropriate technique of corn-legume intercropping in conjunction with the supplemental use of chemical fertilizers, organic manure, and biofertilizers (BFs). Acetylene reduction assays (ARAs) were also performed on corn and soybean roots. Results Combining chemical fertilizers with chicken manure (CM) in a 50:50 ratio and applying 50% NPK+50% CM+BF produced fresh forage and dry matter (DM) yields that were similar to those produced in the 100% nitrogen (N), phosphorus (P), potassium (K) treatment. Among the lone fertilizer treatments, the inorganic fertilizer (100% NPK) treatment produced the highest DM yield (13.86 t/ha) of forage and outyielded the 100% CM (9.74 t/ha) treatment. However, when CM was combined with NPK, the resulting DM yield of forage (13.86 t/ha) was the same as that resulting from 100% NPK (13.68 t/ha). Compared with CM applications alone, combinations of NPK and CM applications resulted in increased plant height, crop growth rates (CGRs) and leaf area index (LAI), but the values of these parameters were similar to those resulting from 100% NPK application. Fertilizers in which the ratio was 50% CM+50% NPK or 50% CM+50% NPK+BF resulted in protein yields that were similar to those resulting from conventional fertilizers. Similarly, the CP content did not significantly differ between applications of the 100% NPK and 50% CM+50% NPK fertilizers. The use of BFs had no significant impact on improving either the yield or quality of forage fertilized with inorganic or organic fertilizer. Lactic acid responded differently to different fertilizer applications and was significantly higher in the fertilized plots t…
bibliographic citation: Baghdadi et al. (2018) Impact of organic and inorganic fertilizers on the yield and quality of silage corn intercropped with soybean. PeerJ 6:e5280 https://doi.org/10.7717/peerj.5280
date submitted: 2018-04-26
date accepted: 2018-07-02
issued: 2018-10-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Baghdadi
  given name: Ali
author list: Agent
  family name: Halim
  given name: Ridzwan A.
author list: Agent
  family name: Ghasemzadeh
  given name: Ali
author list: Agent
  family name: Ramlan
  given name: Mohd Fauzi
author list: Agent
  family name: Sakimin
  given name: Siti Zaharah
doi: 10.7717/peerj.5280
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-26
copyright: ©2018 Baghdadi et al.
attribution name: Baghdadi et al.

Estimation of antimicrobial activities and fatty acid composition of actinobacteria isolated from water surface of underground lakes from Badzheyskaya and Okhotnichya caves in Siberia
type: item
type: AcademicArticle
description: Extreme and unusual ecosystems such as isolated ancient caves are considered as potential tools for the discovery of novel natural products with biological activities. Actinobacteria that inhabit these unusual ecosystems are examined as a promising source for the development of new drugs. In this study we focused on the preliminary estimation of fatty acid composition and antibacterial properties of culturable actinobacteria isolated from water surface of underground lakes located in Badzheyskaya and Okhotnichya caves in Siberia. Here we present isolation of 17 strains of actinobacteria that belong to the Streptomyces, Nocardia and Nocardiopsis genera. Using assays for antibacterial and antifungal activities, we found that a number of strains belonging to the genus Streptomyces isolated from Badzheyskaya cave demonstrated inhibition activity against bacteria and fungi. It was shown that representatives of the genera Nocardia and Nocardiopsis isolated from Okhotnichya cave did not demonstrate any tested antibiotic properties. However, despite the lack of antimicrobial and fungicidal activity of Nocardia extracts, those strains are specific in terms of their fatty acid spectrum. When assessing fatty acid profile, we found that polyunsaturated fatty acids were quantitatively dominant in extracts of Nocardia sp. and Streptomyces sp. grown in different media. Saturated fatty acids were the second most abundant type in the fatty acid profile. It was due to palmitic acid. Also, a few monounsaturated fatty acids were detected. The obtained materials can become a basis for development of approaches to use bacteria isolated from caves as a biological sources of bioactive compounds to create medical and veterinary drugs.
format: application/pdf
format: text/html
creator: Irina V. Voytsekhovskaya
creator: Denis V. Axenov-Gribanov
creator: Svetlana A. Murzina
creator: Svetlana N. Pekkoeva
creator: Eugeniy S. Protasov
creator: Stanislav V. Gamaiunov
creator: Maxim A. Timofeyev
subject: Agricultural Science
subject: Biodiversity
subject: Ecology
subject: Microbiology
subject: Freshwater Biology
description: doi:10.7717/peerj.5832
publisher: PeerJ Inc.
rights: © 2018 Voytsekhovskaya et al.
abstract: Extreme and unusual ecosystems such as isolated ancient caves are considered as potential tools for the discovery of novel natural products with biological activities. Actinobacteria that inhabit these unusual ecosystems are examined as a promising source for the development of new drugs. In this study we focused on the preliminary estimation of fatty acid composition and antibacterial properties of culturable actinobacteria isolated from water surface of underground lakes located in Badzheyskaya and Okhotnichya caves in Siberia. Here we present isolation of 17 strains of actinobacteria that belong to the Streptomyces, Nocardia and Nocardiopsis genera. Using assays for antibacterial and antifungal activities, we found that a number of strains belonging to the genus Streptomyces isolated from Badzheyskaya cave demonstrated inhibition activity against bacteria and fungi. It was shown that representatives of the genera Nocardia and Nocardiopsis isolated from Okhotnichya cave did not demonstrate any tested antibiotic properties. However, despite the lack of antimicrobial and fungicidal activity of Nocardia extracts, those strains are specific in terms of their fatty acid spectrum. When assessing fatty acid profile, we found that polyunsaturated fatty acids were quantitatively dominant in extracts of Nocardia sp. and Streptomyces sp. grown in different media. Saturated fatty acids were the second most abundant type in the fatty acid profile. It was due to palmitic acid. Also, a few monounsaturated fatty acids were detected. The obtained materials can become a basis for development of approaches to use bacteria isolated from caves as a biological sources of bioactive compounds to create medical and veterinary drugs.
bibliographic citation: Voytsekhovskaya et al. (2018) Estimation of antimicrobial activities and fatty acid composition of actinobacteria isolated from water surface of underground lakes from Badzheyskaya and Okhotnichya caves in Siberia. PeerJ 6:e5832 https://doi.org/10.7717/peerj.5832
date submitted: 2018-05-23
date accepted: 2018-09-24
issued: 2018-10-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Voytsekhovskaya
  given name: Irina V.
author list: Agent
  family name: Axenov-Gribanov
  given name: Denis V.
author list: Agent
  family name: Murzina
  given name: Svetlana A.
author list: Agent
  family name: Pekkoeva
  given name: Svetlana N.
author list: Agent
  family name: Protasov
  given name: Eugeniy S.
author list: Agent
  family name: Gamaiunov
  given name: Stanislav V.
author list: Agent
  family name: Timofeyev
  given name: Maxim A.
doi: 10.7717/peerj.5832
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-25
copyright: ©2018 Voytsekhovskaya et al.
attribution name: Voytsekhovskaya et al.

PeerJ
type: Periodical
uri: PeerJ
issn: 2167-8359