PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Constitution of a comprehensive phytochemical profile and network pharmacology based investigation to decipher molecular mechanisms of Teucrium polium L. in the treatment of type 2 diabetes mellitus
items: Pseudodiaptomus marinus Sato, 1913 in the Black Sea: morphology, genetic analysis, and variability in seasonal and interannual abundance
items: Using ForeStereo and LIDAR data to assess fire and canopy structure-related risks in relict Abies pinsapo Boiss. forests
items: Older adults at high risk of HIV infection in China: a systematic review and meta-analysis of observational studies
items: De novo species identification using 16S rRNA gene nanopore sequencing
items: Small-scale distribution of microbes and biogeochemistry in the Great Barrier Reef
items: Comparison of the diversity of cultured and total bacterial communities in marine sediment using culture-dependent and sequencing methods
items: Functional characterization of quorum sensing LuxR-type transcriptional regulator, EasR in Enterobacter asburiae strain L1
items: Morphological and molecular systematic review of Marphysa Quatrefages, 1865 (Annelida: Eunicidae) species from South Africa
items: Vegetation drives the structure of active microbial communities on an acidogenic mine tailings deposit

Constitution of a comprehensive phytochemical profile and network pharmacology based investigation to decipher molecular mechanisms of Teucrium polium L. in the treatment of type 2 diabetes mellitus
type: item
type: AcademicArticle
description: Background Type 2 diabetes mellitus (T2DM) is a metabolic disease affecting a huge population worldwide. Teucrium polium L. has been used as a folk medicine for the treatment of T2DM in Anatolia, Turkey. The antihyperglycemic effect of the plant was reported previously. However, there was no detailed study on the underlying molecular mechanisms. In this study, we generated a research plan to clarify the active constituents of the extract and uncover the molecular mechanisms using network pharmacology analysis. Methods For this purpose, we composed a dataset of 126 compounds for the phytochemical profile of the aerial parts of T. polium. Drug-likeness of the compounds was evaluated, and 52 compounds were selected for further investigation. A total of 252 T2DM related targets hit by selected compounds were subjected to DAVID database. Results The KEGG pathway analysis showed enrichment for the TNF signaling pathway, insulin resistance, the HIF-1 signaling pathway, apoptosis, the PI3K-AKT signaling pathway, the FOXO signaling pathway, the insulin signaling pathway, and type 2 diabetes mellitus which are related to T2DM . AKT1, IL6, STAT3, TP53, INS, and VEGFA were found to be key targets in protein-protein interaction. Besides these key targets, with this study the role of GSK3β, GLUT4, and PDX1 were also discussed through literature and considered as important targets in the antidiabetic effect of T. polium. Various compounds of T. polium were shown to interact with the key targets activating PI3K-AKT and insulin signaling pathways. Conclusions According to these findings, mainly phenolic compounds were identified as the active components and IRS1/PI3K/AKT signaling and insulin resistance were identified as the main pathways regulated by T. polium. This study reveals the relationship of the compounds in T. polium with the targets of T2DM in human. Our findings suggested the use of T. polium as an effective herbal drug in the treatment of T2DM and provides new insights…
format: application/pdf
format: text/html
creator: Vahap Murat Kutluay
creator: Neziha Yagmur Diker
subject: Bioinformatics
subject: Plant Science
subject: Diabetes and Endocrinology
subject: Drugs and Devices
subject: Pharmacology
description: doi:10.7717/peerj.10111
publisher: PeerJ Inc.
rights: © 2020 Kutluay and Diker
abstract: Background Type 2 diabetes mellitus (T2DM) is a metabolic disease affecting a huge population worldwide. Teucrium polium L. has been used as a folk medicine for the treatment of T2DM in Anatolia, Turkey. The antihyperglycemic effect of the plant was reported previously. However, there was no detailed study on the underlying molecular mechanisms. In this study, we generated a research plan to clarify the active constituents of the extract and uncover the molecular mechanisms using network pharmacology analysis. Methods For this purpose, we composed a dataset of 126 compounds for the phytochemical profile of the aerial parts of T. polium. Drug-likeness of the compounds was evaluated, and 52 compounds were selected for further investigation. A total of 252 T2DM related targets hit by selected compounds were subjected to DAVID database. Results The KEGG pathway analysis showed enrichment for the TNF signaling pathway, insulin resistance, the HIF-1 signaling pathway, apoptosis, the PI3K-AKT signaling pathway, the FOXO signaling pathway, the insulin signaling pathway, and type 2 diabetes mellitus which are related to T2DM . AKT1, IL6, STAT3, TP53, INS, and VEGFA were found to be key targets in protein-protein interaction. Besides these key targets, with this study the role of GSK3β, GLUT4, and PDX1 were also discussed through literature and considered as important targets in the antidiabetic effect of T. polium. Various compounds of T. polium were shown to interact with the key targets activating PI3K-AKT and insulin signaling pathways. Conclusions According to these findings, mainly phenolic compounds were identified as the active components and IRS1/PI3K/AKT signaling and insulin resistance were identified as the main pathways regulated by T. polium. This study reveals the relationship of the compounds in T. polium with the targets of T2DM in human. Our findings suggested the use of T. polium as an effective herbal drug in the treatment of T2DM and provides new insights…
bibliographic citation: Kutluay et al. (2020) Constitution of a comprehensive phytochemical profile and network pharmacology based investigation to decipher molecular mechanisms of Teucrium polium L. in the treatment of type 2 diabetes mellitus. PeerJ 8:e10111 https://doi.org/10.7717/peerj.10111
date submitted: 2020-07-08
date accepted: 2020-09-16
issued: 2020-10-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kutluay
  given name: Vahap Murat
author list: Agent
  family name: Diker
  given name: Neziha Yagmur
doi: 10.7717/peerj.10111
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-22
copyright: ©2020 Kutluay and Diker
attribution name: Kutluay and Diker

Pseudodiaptomus marinus Sato, 1913 in the Black Sea: morphology, genetic analysis, and variability in seasonal and interannual abundance
type: item
type: AcademicArticle
description: Calanoid copepod Peudodiaptomus marinus Sato, 1913 was first recorded in Sevastopol Bay in the northern Black Sea in September 2016. We performed regular observations of this new invasive species between October 2016 and December 2018. We conducted bi-weekly plankton sampling at three stations located within or adjacent to Sevastopol Bay. This is the first paper to combine (i) a detailed morphological study, (ii) molecular genetic analysis, and (iii) an investigation of P. marinus seasonal dynamics and interannual abundance variability in the coastal Black Sea. Our morphological research showed similarities between Pseudodiaptomus specimens and existing P. marinus illustrations and descriptions. Our morphological analysis results were confirmed using molecular genetic studies. Based on the genetic variability of ITS2 and cytb, we found that all investigated specimens from Sevastopol Bay belonged to P. marinus. Investigations of P. marinus seasonal and interannual abundance variability showed the same seasonal patterns throughout the studied period, with a higher seasonal abundance from October to November and one pronounced density peak in autumn. The highest abundances (2,000 ind m–3 at the mouth of the bay and more than 5,000 ind m–3at its centre) were recorded in November 2018. In the samples, we found adults of both sexes, including ovigerous females, copepodites I–V, and nauplii, suggesting that the species reproduce in Sevastopol Bay. Our research indicated that P. marinus is a new non-indigenous species (NIS) in the Black Sea, and we will discuss a possible vector of its introduction into this basin.
format: application/pdf
format: text/html
creator: Alexandra Gubanova
creator: Inna Drapun
creator: Oksana Garbazey
creator: Olga Krivenko
creator: Ekaterina Vodiasova
subject: Ecology
subject: Biodiversity
subject: Marine Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.10153
publisher: PeerJ Inc.
rights: © 2020 Gubanova et al.
abstract: Calanoid copepod Peudodiaptomus marinus Sato, 1913 was first recorded in Sevastopol Bay in the northern Black Sea in September 2016. We performed regular observations of this new invasive species between October 2016 and December 2018. We conducted bi-weekly plankton sampling at three stations located within or adjacent to Sevastopol Bay. This is the first paper to combine (i) a detailed morphological study, (ii) molecular genetic analysis, and (iii) an investigation of P. marinus seasonal dynamics and interannual abundance variability in the coastal Black Sea. Our morphological research showed similarities between Pseudodiaptomus specimens and existing P. marinus illustrations and descriptions. Our morphological analysis results were confirmed using molecular genetic studies. Based on the genetic variability of ITS2 and cytb, we found that all investigated specimens from Sevastopol Bay belonged to P. marinus. Investigations of P. marinus seasonal and interannual abundance variability showed the same seasonal patterns throughout the studied period, with a higher seasonal abundance from October to November and one pronounced density peak in autumn. The highest abundances (2,000 ind m–3 at the mouth of the bay and more than 5,000 ind m–3at its centre) were recorded in November 2018. In the samples, we found adults of both sexes, including ovigerous females, copepodites I–V, and nauplii, suggesting that the species reproduce in Sevastopol Bay. Our research indicated that P. marinus is a new non-indigenous species (NIS) in the Black Sea, and we will discuss a possible vector of its introduction into this basin.
bibliographic citation: Gubanova et al. (2020) Pseudodiaptomus marinus Sato, 1913 in the Black Sea: morphology, genetic analysis, and variability in seasonal and interannual abundance. PeerJ 8:e10153 https://doi.org/10.7717/peerj.10153
date submitted: 2020-01-16
date accepted: 2020-09-21
issued: 2020-10-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gubanova
  given name: Alexandra
author list: Agent
  family name: Drapun
  given name: Inna
author list: Agent
  family name: Garbazey
  given name: Oksana
author list: Agent
  family name: Krivenko
  given name: Olga
author list: Agent
  family name: Vodiasova
  given name: Ekaterina
doi: 10.7717/peerj.10153
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-22
copyright: ©2020 Gubanova et al.
attribution name: Gubanova et al.

Using ForeStereo and LIDAR data to assess fire and canopy structure-related risks in relict Abies pinsapo Boiss. forests
type: item
type: AcademicArticle
description: In this study we combine information from aerial LIDAR and hemispherical images taken in the field with ForeStereo—a forest inventory device—to assess the vulnerability and to design conservation strategies for endangered Mediterranean fir forests based on the mapping of fire risk and canopy structure spatial variability. We focused on the largest continuous remnant population of the endangered tree species Abies pinsapo Boiss. spanning 252 ha in Sierra de las Nieves National Park (South Andalusia, Spain). We established 49 sampling plots over the study area. Stand structure variables were derived from ForeStereo device, a proximal sensing technology for tree diameter, height and crown dimensions and stand crown cover and basal area retrieval from stereoscopic hemispherical images photogrammetry. With this information, we developed regression models with airborne LIDAR data (spatial resolution of 0.5 points∙m−2). Thereafter, six fuel models were fitted to the plots according to the UCO40 classification criteria, and then the entire area was classified using the Nearest Neighbor algorithm on Sentinel imagery (overall accuracy of 0.56 and a KIA-Kappa Coefficient of 0.46). FlamMap software was used for fire simulation scenarios based on fuel models, stand structure, and terrain data. Besides the fire simulation, we analyzed canopy structure to assess the status and vulnerability of this fir population. The assessment shows a secondary growth forest that has an increasing presence of fuel models with the potential for high fire spread rate fire and burn probability. Our methodological approach has the potential to be integrated as a support tool for the adaptive management and conservation of A. pinsapo across its whole distribution area (<4,000 ha), as well as for other endangered circum-Mediterranean fir forests, as A. numidica de Lannoy and A. pinsapo marocana Trab. in North Africa.
format: application/pdf
format: text/html
creator: Álvaro Cortés-Molino
creator: Isabel Aulló-Maestro
creator: Ismael Fernandez-Luque
creator: Antonio Flores-Moya
creator: José A. Carreira
creator: A. Enrique Salvo
subject: Ecosystem Science
subject: Climate Change Biology
subject: Natural Resource Management
subject: Environmental Impacts
subject: Forestry
description: doi:10.7717/peerj.10158
publisher: PeerJ Inc.
rights: © 2020 Cortés-Molino et al.
abstract: In this study we combine information from aerial LIDAR and hemispherical images taken in the field with ForeStereo—a forest inventory device—to assess the vulnerability and to design conservation strategies for endangered Mediterranean fir forests based on the mapping of fire risk and canopy structure spatial variability. We focused on the largest continuous remnant population of the endangered tree species Abies pinsapo Boiss. spanning 252 ha in Sierra de las Nieves National Park (South Andalusia, Spain). We established 49 sampling plots over the study area. Stand structure variables were derived from ForeStereo device, a proximal sensing technology for tree diameter, height and crown dimensions and stand crown cover and basal area retrieval from stereoscopic hemispherical images photogrammetry. With this information, we developed regression models with airborne LIDAR data (spatial resolution of 0.5 points∙m−2). Thereafter, six fuel models were fitted to the plots according to the UCO40 classification criteria, and then the entire area was classified using the Nearest Neighbor algorithm on Sentinel imagery (overall accuracy of 0.56 and a KIA-Kappa Coefficient of 0.46). FlamMap software was used for fire simulation scenarios based on fuel models, stand structure, and terrain data. Besides the fire simulation, we analyzed canopy structure to assess the status and vulnerability of this fir population. The assessment shows a secondary growth forest that has an increasing presence of fuel models with the potential for high fire spread rate fire and burn probability. Our methodological approach has the potential to be integrated as a support tool for the adaptive management and conservation of A. pinsapo across its whole distribution area (<4,000 ha), as well as for other endangered circum-Mediterranean fir forests, as A. numidica de Lannoy and A. pinsapo marocana Trab. in North Africa.
bibliographic citation: Cortés-Molino et al. (2020) Using ForeStereo and LIDAR data to assess fire and canopy structure-related risks in relict Abies pinsapo Boiss. forests. PeerJ 8:e10158 https://doi.org/10.7717/peerj.10158
date submitted: 2020-03-03
date accepted: 2020-09-21
issued: 2020-10-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cortés-Molino
  given name: Álvaro
author list: Agent
  family name: Aulló-Maestro
  given name: Isabel
author list: Agent
  family name: Fernandez-Luque
  given name: Ismael
author list: Agent
  family name: Flores-Moya
  given name: Antonio
author list: Agent
  family name: Carreira
  given name: José A.
author list: Agent
  family name: Salvo
  given name: A. Enrique
doi: 10.7717/peerj.10158
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-22
copyright: © 2020 Cortés-Molino et al.
attribution name: Cortés-Molino et al.

Older adults at high risk of HIV infection in China: a systematic review and meta-analysis of observational studies
type: item
type: AcademicArticle
description: There is an increasing prevalence of human immunodeficiency virus (HIV) infection in older adults in China, but the findings across prevalence studies have been mixed. This is the first meta-analysis of the prevalence of HIV infection and its moderating factors in older adults in China. Two investigators systematically and independently searched both international (PubMed, PsycINFO, Web of Sciences and EMBASE) and Chinese (WanFang, CNKI, and CQVIP) databases. HIV infection rates in older adults were analyzed using the random-effects model. Altogether 46 studies were included in the analysis. The pooled prevalence of HIV infection in older adults was 2.1% (95% CI [1.9%–2.3%], I2 = 99.4%). Subgroup analyses revealed that men who have sex with men (MSM), hospital population samples, publications after 2014, studies conducted in the western region of China, and higher study quality were significantly associated with higher HIV infection rate. This meta-analysis found that the HIV infection prevalence in older adults is significantly higher than the general population in China. Attention should be given to this urgent public health issue, and effective HIV/AIDS preventive, screening and treatment measures are warranted in this population. PROSPERO: CRD42019124286.
format: application/pdf
format: text/html
creator: Yuan Yuan Wang
creator: Yuan Yang
creator: Chang Chen
creator: Ling Zhang
creator: Chee H. Ng
creator: Gabor S. Ungvari
creator: Xiaohua Douglas Zhang
creator: Yu-Tao Xiang
subject: HIV
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.9731
publisher: PeerJ Inc.
rights: © 2020 Wang et al.
abstract: There is an increasing prevalence of human immunodeficiency virus (HIV) infection in older adults in China, but the findings across prevalence studies have been mixed. This is the first meta-analysis of the prevalence of HIV infection and its moderating factors in older adults in China. Two investigators systematically and independently searched both international (PubMed, PsycINFO, Web of Sciences and EMBASE) and Chinese (WanFang, CNKI, and CQVIP) databases. HIV infection rates in older adults were analyzed using the random-effects model. Altogether 46 studies were included in the analysis. The pooled prevalence of HIV infection in older adults was 2.1% (95% CI [1.9%–2.3%], I2 = 99.4%). Subgroup analyses revealed that men who have sex with men (MSM), hospital population samples, publications after 2014, studies conducted in the western region of China, and higher study quality were significantly associated with higher HIV infection rate. This meta-analysis found that the HIV infection prevalence in older adults is significantly higher than the general population in China. Attention should be given to this urgent public health issue, and effective HIV/AIDS preventive, screening and treatment measures are warranted in this population. PROSPERO: CRD42019124286.
bibliographic citation: Wang et al. (2020) Older adults at high risk of HIV infection in China: a systematic review and meta-analysis of observational studies. PeerJ 8:e9731 https://doi.org/10.7717/peerj.9731
date submitted: 2020-02-05
date accepted: 2020-07-24
issued: 2020-10-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Yuan Yuan
author list: Agent
  family name: Yang
  given name: Yuan
author list: Agent
  family name: Chen
  given name: Chang
author list: Agent
  family name: Zhang
  given name: Ling
author list: Agent
  family name: Ng
  given name: Chee H.
author list: Agent
  family name: Ungvari
  given name: Gabor S.
author list: Agent
  family name: Zhang
  given name: Xiaohua Douglas
author list: Agent
  family name: Xiang
  given name: Yu-Tao
doi: 10.7717/peerj.9731
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-21
copyright: ©2020 Wang et al.
attribution name: Wang et al.

De novo species identification using 16S rRNA gene nanopore sequencing
type: item
type: AcademicArticle
description: Nanopore sequencing is rapidly becoming more popular for use in various microbiota-based applications. Major limitations of current approaches are that they do not enable de novo species identification and that they cannot be used to verify species assignments. This severely limits applicability of the nanopore sequencing technology in taxonomic applications. Here, we demonstrate the possibility of de novo species identification and verification using hexamer frequencies in combination with k-means clustering for nanopore sequencing data. The approach was tested on the human infant gut microbiota of 3-month-old infants. Using the hexamer k-means approach we identified two new low abundant species associated with vaginal delivery. In addition, we confirmed both the vaginal delivery association for two previously identified species and the overall high levels of bifidobacteria. Taxonomic assignments were further verified by mock community analyses. Therefore, we believe our de novo species identification approach will have widespread application in analyzing microbial communities in the future.
format: application/pdf
format: text/html
creator: Inga Leena Angell
creator: Morten Nilsen
creator: Karin C. Lødrup Carlsen
creator: Kai-Håkon Carlsen
creator: Gunilla Hedlin
creator: Christine M. Jonassen
creator: Benjamin Marsland
creator: Björn Nordlund
creator: Eva Maria Rehbinder
creator: Carina Saunders
creator: Håvard Ove Skjerven
creator: Anne Cathrine Staff
creator: Cilla Söderhäll
creator: Riyas Vettukattil
creator: Knut Rudi
subject: Bioinformatics
subject: Ecology
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.10029
publisher: PeerJ Inc.
rights: © 2020 Angell et al.
abstract: Nanopore sequencing is rapidly becoming more popular for use in various microbiota-based applications. Major limitations of current approaches are that they do not enable de novo species identification and that they cannot be used to verify species assignments. This severely limits applicability of the nanopore sequencing technology in taxonomic applications. Here, we demonstrate the possibility of de novo species identification and verification using hexamer frequencies in combination with k-means clustering for nanopore sequencing data. The approach was tested on the human infant gut microbiota of 3-month-old infants. Using the hexamer k-means approach we identified two new low abundant species associated with vaginal delivery. In addition, we confirmed both the vaginal delivery association for two previously identified species and the overall high levels of bifidobacteria. Taxonomic assignments were further verified by mock community analyses. Therefore, we believe our de novo species identification approach will have widespread application in analyzing microbial communities in the future.
bibliographic citation: Angell et al. (2020) De novo species identification using 16S rRNA gene nanopore sequencing. PeerJ 8:e10029 https://doi.org/10.7717/peerj.10029
date submitted: 2020-03-13
date accepted: 2020-09-03
issued: 2020-10-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Angell
  given name: Inga Leena
author list: Agent
  family name: Nilsen
  given name: Morten
author list: Agent
  family name: Carlsen
  given name: Karin C. Lødrup
author list: Agent
  family name: Carlsen
  given name: Kai-Håkon
author list: Agent
  family name: Hedlin
  given name: Gunilla
author list: Agent
  family name: Jonassen
  given name: Christine M.
author list: Agent
  family name: Marsland
  given name: Benjamin
author list: Agent
  family name: Nordlund
  given name: Björn
author list: Agent
  family name: Rehbinder
  given name: Eva Maria
author list: Agent
  family name: Saunders
  given name: Carina
author list: Agent
  family name: Skjerven
  given name: Håvard Ove
author list: Agent
  family name: Staff
  given name: Anne Cathrine
author list: Agent
  family name: Söderhäll
  given name: Cilla
author list: Agent
  family name: Vettukattil
  given name: Riyas
author list: Agent
  family name: Rudi
  given name: Knut
doi: 10.7717/peerj.10029
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-21
copyright: ©2020 Angell et al.
attribution name: Angell et al.

Small-scale distribution of microbes and biogeochemistry in the Great Barrier Reef
type: item
type: AcademicArticle
description: Microbial communities distribute heterogeneously at small-scales (mm-cm) due to physical, chemical and biological processes. To understand microbial processes and functions it is necessary to appreciate microbes and matter at small scales, however, few studies have determined microbial, viral, and biogeochemical distribution over space and time at these scales. In this study, the small-scale spatial and temporal distribution of microbes (bacteria and chlorophyll a), viruses, dissolved inorganic nutrients and dissolved organic carbon were determined at five locations (spatial) along the Great Barrier Reef (Australia), and over 4 consecutive days (temporal) at a coastal location. Our results show that: (1) the parameters show high small-scale heterogeneity; (2) none of the parameters measured explained the bacterial abundance distributions at these scales spatially or temporally; (3) chemical (ammonium, nitrate/nitrite, phosphate, dissolved organic carbon, and total dissolved nitrogen) and biological (chl a, and bacterial and viral abundances) measurements did not reveal significant relationships at the small scale; and (4) statistically significant differences were found between sites/days for all parameter measured but without a clear pattern.
format: application/pdf
format: text/html
creator: Cátia Carreira
creator: Júlia Porto Silva Carvalho
creator: Samantha Talbot
creator: Isabel Pereira
creator: Christian Lønborg
subject: Ecology
subject: Microbiology
subject: Aquatic and Marine Chemistry
subject: Biological Oceanography
description: doi:10.7717/peerj.10049
publisher: PeerJ Inc.
rights: © 2020 Carreira et al.
abstract: Microbial communities distribute heterogeneously at small-scales (mm-cm) due to physical, chemical and biological processes. To understand microbial processes and functions it is necessary to appreciate microbes and matter at small scales, however, few studies have determined microbial, viral, and biogeochemical distribution over space and time at these scales. In this study, the small-scale spatial and temporal distribution of microbes (bacteria and chlorophyll a), viruses, dissolved inorganic nutrients and dissolved organic carbon were determined at five locations (spatial) along the Great Barrier Reef (Australia), and over 4 consecutive days (temporal) at a coastal location. Our results show that: (1) the parameters show high small-scale heterogeneity; (2) none of the parameters measured explained the bacterial abundance distributions at these scales spatially or temporally; (3) chemical (ammonium, nitrate/nitrite, phosphate, dissolved organic carbon, and total dissolved nitrogen) and biological (chl a, and bacterial and viral abundances) measurements did not reveal significant relationships at the small scale; and (4) statistically significant differences were found between sites/days for all parameter measured but without a clear pattern.
bibliographic citation: Carreira et al. (2020) Small-scale distribution of microbes and biogeochemistry in the Great Barrier Reef. PeerJ 8:e10049 https://doi.org/10.7717/peerj.10049
date submitted: 2020-04-08
date accepted: 2020-09-06
issued: 2020-10-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Carreira
  given name: Cátia
author list: Agent
  family name: Carvalho
  given name: Júlia Porto Silva
author list: Agent
  family name: Talbot
  given name: Samantha
author list: Agent
  family name: Pereira
  given name: Isabel
author list: Agent
  family name: Lønborg
  given name: Christian
doi: 10.7717/peerj.10049
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-21
copyright: ©2020 Carreira et al.
attribution name: Carreira et al.

Comparison of the diversity of cultured and total bacterial communities in marine sediment using culture-dependent and sequencing methods
type: item
type: AcademicArticle
description: Despite recent great advances in microbial culture, most microbes have not yet been cultured, and the impact of medium composition on the isolation of microbes from natural systems has not been elucidated. To optimize media for culturing marine microbes, microbial communities in three sediment samples were described using high-throughput sequencing (HTS) and culture-dependent techniques. HTS revealed communities dominated by Gammaproteobacteria, and culture-based methods revealed communities dominated by Actinobacteria. Among the total operational taxonomic units (OTUs) from the HTS dataset, 6% were recovered in the culture collection. Four potentially novel bacterial strains belonging to Oceaniovalibus, Psychrobacter and Salegentibacter were isolated. The combination of media cultured more taxa than any single medium. Nutrient-rich and single-carbon/nitrogen-source media supported the growth of relatively few taxa, and the quality of nitrogen strongly influenced the types of bacteria isolated.
format: application/pdf
format: text/html
creator: Meng Wang
creator: Samina Noor
creator: Ran Huan
creator: Congling Liu
creator: JiaYi Li
creator: Qingxin Shi
creator: Yan-Jiao Zhang
creator: Cuiling Wu
creator: Hailun He
subject: Biotechnology
subject: Marine Biology
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.10060
publisher: PeerJ Inc.
rights: © 2020 Wang et al.
abstract: Despite recent great advances in microbial culture, most microbes have not yet been cultured, and the impact of medium composition on the isolation of microbes from natural systems has not been elucidated. To optimize media for culturing marine microbes, microbial communities in three sediment samples were described using high-throughput sequencing (HTS) and culture-dependent techniques. HTS revealed communities dominated by Gammaproteobacteria, and culture-based methods revealed communities dominated by Actinobacteria. Among the total operational taxonomic units (OTUs) from the HTS dataset, 6% were recovered in the culture collection. Four potentially novel bacterial strains belonging to Oceaniovalibus, Psychrobacter and Salegentibacter were isolated. The combination of media cultured more taxa than any single medium. Nutrient-rich and single-carbon/nitrogen-source media supported the growth of relatively few taxa, and the quality of nitrogen strongly influenced the types of bacteria isolated.
bibliographic citation: Wang et al. (2020) Comparison of the diversity of cultured and total bacterial communities in marine sediment using culture-dependent and sequencing methods. PeerJ 8:e10060 https://doi.org/10.7717/peerj.10060
date submitted: 2020-01-29
date accepted: 2020-09-07
issued: 2020-10-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Meng
author list: Agent
  family name: Noor
  given name: Samina
author list: Agent
  family name: Huan
  given name: Ran
author list: Agent
  family name: Liu
  given name: Congling
author list: Agent
  family name: Li
  given name: JiaYi
author list: Agent
  family name: Shi
  given name: Qingxin
author list: Agent
  family name: Zhang
  given name: Yan-Jiao
author list: Agent
  family name: Wu
  given name: Cuiling
author list: Agent
  family name: He
  given name: Hailun
doi: 10.7717/peerj.10060
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-21
copyright: ©2020 Wang et al.
attribution name: Wang et al.

Functional characterization of quorum sensing LuxR-type transcriptional regulator, EasR in Enterobacter asburiae strain L1
type: item
type: AcademicArticle
description: Over the past decades, Enterobacter spp. have been identified as challenging and important pathogens. The emergence of multidrug-resistant Enterobacteria especially those that produce Klebsiella pneumoniae carbapenemase has been a very worrying health crisis. Although efforts have been made to unravel the complex mechanisms that contribute to the pathogenicity of different Enterobacter spp., there is very little information associated with AHL-type QS mechanism in Enterobacter spp. Signaling via N-acyl homoserine lactone (AHL) is the most common quorum sensing (QS) mechanism utilized by Proteobacteria. A typical AHL-based QS system involves two key players: a luxI gene homolog to synthesize AHLs and a luxR gene homolog, an AHL-dependent transcriptional regulator. These signaling molecules enable inter-species and intra-species interaction in response to external stimuli according to population density. In our recent study, we reported the genome of AHL-producing bacterium, Enterobacter asburiae strain L1. Whole genome sequencing and in silico analysis revealed the presence of a pair of luxI/R genes responsible for AHL-type QS, designated as easI/R, in strain L1. In a QS system, a LuxR transcriptional protein detects and responds to the concentration of a specific AHL controlling gene expression. In E. asburiae strain L1, EasR protein binds to its cognate AHLs, N-butanoyl homoserine lactone (C4-HSL) and N–hexanoyl homoserine lactone (C6-HSL), modulating the expression of targeted genes. In this current work, we have cloned the 693 bp luxR homolog of strain L1 for further characterization. The functionality and specificity of EasR protein in response to different AHL signaling molecules to activate gene transcription were tested and validated with β-galactosidase assays. Higher β-galactosidase activities were detected for cells harboring EasR, indicating EasR is a functional transcriptional regulator. This is the first report documenting the cloning and characterizati…
format: application/pdf
format: text/html
creator: Yin Yin Lau
creator: Kah Yan How
creator: Wai-Fong Yin
creator: Kok-Gan Chan
subject: Genomics
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.10068
publisher: PeerJ Inc.
rights: © 2020 Lau et al.
abstract: Over the past decades, Enterobacter spp. have been identified as challenging and important pathogens. The emergence of multidrug-resistant Enterobacteria especially those that produce Klebsiella pneumoniae carbapenemase has been a very worrying health crisis. Although efforts have been made to unravel the complex mechanisms that contribute to the pathogenicity of different Enterobacter spp., there is very little information associated with AHL-type QS mechanism in Enterobacter spp. Signaling via N-acyl homoserine lactone (AHL) is the most common quorum sensing (QS) mechanism utilized by Proteobacteria. A typical AHL-based QS system involves two key players: a luxI gene homolog to synthesize AHLs and a luxR gene homolog, an AHL-dependent transcriptional regulator. These signaling molecules enable inter-species and intra-species interaction in response to external stimuli according to population density. In our recent study, we reported the genome of AHL-producing bacterium, Enterobacter asburiae strain L1. Whole genome sequencing and in silico analysis revealed the presence of a pair of luxI/R genes responsible for AHL-type QS, designated as easI/R, in strain L1. In a QS system, a LuxR transcriptional protein detects and responds to the concentration of a specific AHL controlling gene expression. In E. asburiae strain L1, EasR protein binds to its cognate AHLs, N-butanoyl homoserine lactone (C4-HSL) and N–hexanoyl homoserine lactone (C6-HSL), modulating the expression of targeted genes. In this current work, we have cloned the 693 bp luxR homolog of strain L1 for further characterization. The functionality and specificity of EasR protein in response to different AHL signaling molecules to activate gene transcription were tested and validated with β-galactosidase assays. Higher β-galactosidase activities were detected for cells harboring EasR, indicating EasR is a functional transcriptional regulator. This is the first report documenting the cloning and characterizati…
bibliographic citation: Lau et al. (2020) Functional characterization of quorum sensing LuxR-type transcriptional regulator, EasR in Enterobacter asburiae strain L1. PeerJ 8:e10068 https://doi.org/10.7717/peerj.10068
date submitted: 2019-11-26
date accepted: 2020-09-08
issued: 2020-10-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lau
  given name: Yin Yin
author list: Agent
  family name: How
  given name: Kah Yan
author list: Agent
  family name: Yin
  given name: Wai-Fong
author list: Agent
  family name: Chan
  given name: Kok-Gan
doi: 10.7717/peerj.10068
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-21
copyright: © 2020 Lau et al.
attribution name: Lau et al.

Morphological and molecular systematic review of Marphysa Quatrefages, 1865 (Annelida: Eunicidae) species from South Africa
type: item
type: AcademicArticle
description: A vast polychaete fauna is hidden behind complexes of cryptic and pseudo-cryptic species, which has greatly hindered our understanding of species diversity in several regions worldwide. Among the eunicids, Marphysa sanguinea Montagu, 1813 is a typical example, recorded in three oceans and with various species considered its junior synonyms. In South Africa, specimens previously misidentified as M. sanguinea are now known as Marphysa elityeni Lewis & Karageorgopoulos, 2008. Of the six Marphysa Quatrefages, 1865a species recorded from the same region, three have their distributions restricted to South Africa while the others are considered to have worldwide distributions. Here, we evaluated the taxonomic status of the indigenous M. elityeni and investigated the presence of the widespread species Marphysa macintoshi Crossland, 1903 and Marphysa depressa Schmarda, 1861 in South Africa using morphological and molecular data. Our results reveal that M. elityeni is a junior synonym of Marphysa haemasoma, a species previously described from South Africa which is herein reinstated as a valid species. Both M. macintoshi and M. depressa are not present in South Africa and their status as being distributed worldwide deserves further investigation. Marphysa durbanensis Day, 1934 and the new species described here, M. sherlockae n. sp., had been misidentified as M. macintoshi and M. depressa respectively. Thus, the number of Marphysa species with distributions restricted to South Africa increased from three to five. This study reiterates the importance of implementing an integrated taxonomic framework to unravel local biodiversity.
format: application/pdf
format: text/html
creator: Jyothi Kara
creator: Isabel C. Molina-Acevedo
creator: Joana Zanol
creator: Carol Simon
creator: Izwandy Idris
subject: Biodiversity
subject: Marine Biology
subject: Molecular Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.10076
publisher: PeerJ Inc.
rights: © 2020 Kara et al.
abstract: A vast polychaete fauna is hidden behind complexes of cryptic and pseudo-cryptic species, which has greatly hindered our understanding of species diversity in several regions worldwide. Among the eunicids, Marphysa sanguinea Montagu, 1813 is a typical example, recorded in three oceans and with various species considered its junior synonyms. In South Africa, specimens previously misidentified as M. sanguinea are now known as Marphysa elityeni Lewis & Karageorgopoulos, 2008. Of the six Marphysa Quatrefages, 1865a species recorded from the same region, three have their distributions restricted to South Africa while the others are considered to have worldwide distributions. Here, we evaluated the taxonomic status of the indigenous M. elityeni and investigated the presence of the widespread species Marphysa macintoshi Crossland, 1903 and Marphysa depressa Schmarda, 1861 in South Africa using morphological and molecular data. Our results reveal that M. elityeni is a junior synonym of Marphysa haemasoma, a species previously described from South Africa which is herein reinstated as a valid species. Both M. macintoshi and M. depressa are not present in South Africa and their status as being distributed worldwide deserves further investigation. Marphysa durbanensis Day, 1934 and the new species described here, M. sherlockae n. sp., had been misidentified as M. macintoshi and M. depressa respectively. Thus, the number of Marphysa species with distributions restricted to South Africa increased from three to five. This study reiterates the importance of implementing an integrated taxonomic framework to unravel local biodiversity.
bibliographic citation: Kara et al. (2020) Morphological and molecular systematic review of Marphysa Quatrefages, 1865 (Annelida: Eunicidae) species from South Africa. PeerJ 8:e10076 https://doi.org/10.7717/peerj.10076
date submitted: 2020-05-19
date accepted: 2020-09-10
issued: 2020-10-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kara
  given name: Jyothi
author list: Agent
  family name: Molina-Acevedo
  given name: Isabel C.
author list: Agent
  family name: Zanol
  given name: Joana
author list: Agent
  family name: Simon
  given name: Carol
author list: Agent
  family name: Idris
  given name: Izwandy
doi: 10.7717/peerj.10076
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-21
copyright: ©2020 Kara et al.
attribution name: Kara et al.

Vegetation drives the structure of active microbial communities on an acidogenic mine tailings deposit
type: item
type: AcademicArticle
description: Plant-microbe associations are increasingly recognized as an inextricable part of plant biology and biogeochemistry. Microbes play an essential role in the survival and development of plants, allowing them to thrive in diverse environments. The composition of the rhizosphere soil microbial communities is largely influenced by edaphic conditions and plant species. In order to decipher how environmental conditions on a mine site can influence the dynamics of microbial communities, we characterized the rhizosphere soil microbial communities associated with paper birch, speckled alder, and spruce that had naturally colonized an acidogenic mine tailings deposit containing heavy metals. The study site, which had been largely undisturbed for five decades, had highly variable vegetation density; with some areas remaining almost barren, and others having a few stands or large thickets of mature trees. Using Illumina sequencing and ordination analyses (redundancy analysis and principal coordinate analysis), our study showed that soil bacterial and fungal community structures correlated mainly with vegetation density, and plant species. Tailings without any vegetation were the most different in bacterial community structure, compared to all other areas on the mine site, as well as an adjacent natural forest (comparison plot). The bacterial genera Acidiferrobacter and Leptospirillum were more abundant in tailings without vegetation than in any of the other sites, while Bradyrhizobium sp. were more abundant in areas of the tailings deposit having higher vegetation density. Frankia sp. is equally represented in each of the vegetation densities and Pseudomonas sp. present a greater relative abundance in boreal forest. Furthermore, alder rhizosphere showed a greater relative abundance of Bradyrhizobium sp. (in comparison with birch and spruce) as well as Haliangium sp. (in comparison with birch). In contrast, fungal community structures were similar across the tailings deposit rega…
format: application/pdf
format: text/html
creator: Vanessa Gagnon
creator: Michaël Rodrigue-Morin
creator: Julien Tremblay
creator: Jessica Wasserscheid
creator: Julie Champagne
creator: Jean-Philippe Bellenger
creator: Charles W. Greer
creator: Sébastien Roy
subject: Microbiology
subject: Biogeochemistry
subject: Environmental Contamination and Remediation
subject: Environmental Impacts
description: doi:10.7717/peerj.10109
publisher: PeerJ Inc.
rights: © 2020 Gagnon et al.
abstract: Plant-microbe associations are increasingly recognized as an inextricable part of plant biology and biogeochemistry. Microbes play an essential role in the survival and development of plants, allowing them to thrive in diverse environments. The composition of the rhizosphere soil microbial communities is largely influenced by edaphic conditions and plant species. In order to decipher how environmental conditions on a mine site can influence the dynamics of microbial communities, we characterized the rhizosphere soil microbial communities associated with paper birch, speckled alder, and spruce that had naturally colonized an acidogenic mine tailings deposit containing heavy metals. The study site, which had been largely undisturbed for five decades, had highly variable vegetation density; with some areas remaining almost barren, and others having a few stands or large thickets of mature trees. Using Illumina sequencing and ordination analyses (redundancy analysis and principal coordinate analysis), our study showed that soil bacterial and fungal community structures correlated mainly with vegetation density, and plant species. Tailings without any vegetation were the most different in bacterial community structure, compared to all other areas on the mine site, as well as an adjacent natural forest (comparison plot). The bacterial genera Acidiferrobacter and Leptospirillum were more abundant in tailings without vegetation than in any of the other sites, while Bradyrhizobium sp. were more abundant in areas of the tailings deposit having higher vegetation density. Frankia sp. is equally represented in each of the vegetation densities and Pseudomonas sp. present a greater relative abundance in boreal forest. Furthermore, alder rhizosphere showed a greater relative abundance of Bradyrhizobium sp. (in comparison with birch and spruce) as well as Haliangium sp. (in comparison with birch). In contrast, fungal community structures were similar across the tailings deposit rega…
bibliographic citation: Gagnon et al. (2020) Vegetation drives the structure of active microbial communities on an acidogenic mine tailings deposit. PeerJ 8:e10109 https://doi.org/10.7717/peerj.10109
date submitted: 2020-03-05
date accepted: 2020-09-16
issued: 2020-10-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gagnon
  given name: Vanessa
author list: Agent
  family name: Rodrigue-Morin
  given name: Michaël
author list: Agent
  family name: Tremblay
  given name: Julien
author list: Agent
  family name: Wasserscheid
  given name: Jessica
author list: Agent
  family name: Champagne
  given name: Julie
author list: Agent
  family name: Bellenger
  given name: Jean-Philippe
author list: Agent
  family name: Greer
  given name: Charles W.
author list: Agent
  family name: Roy
  given name: Sébastien
doi: 10.7717/peerj.10109
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-21
copyright: ©2020 Gagnon et al.
attribution name: Gagnon et al.

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