scholarly journals Estimation of the relative abundance of species in artificial mixtures of insects using low-coverage shotgun metagenomics

2020 ◽  
Vol 4 ◽  
Author(s):  
Lidia Garrido-Sanz ◽  
Miquel Àngel Senar ◽  
Josep Piñol
Keyword(s):  
Relative Abundance ◽  
Species Abundance ◽  
Single Species ◽  
Insect Species ◽  
Individual Species ◽  
Advanced Degree ◽  
Mixed Species ◽  
Species List ◽  
Shotgun Metagenomics ◽  
Low Coverage

Amplicon metabarcoding is an established technique to analyse the taxonomic composition of communities of organisms using high-throughput DNA sequencing, but there are doubts about its ability to quantify the relative proportions of the species, as opposed to the species list. Here, we bypass the enrichment step and avoid the PCR-bias, by directly sequencing the extracted DNA using shotgun metagenomics. This approach is common practice in prokaryotes, but not in eukaryotes, because of the low number of sequenced genomes of eukaryotic species. We tested the metagenomics approach using insect species whose genome is already sequenced and assembled to an advanced degree. We shotgun-sequenced, at low-coverage, 18 species of insects in 22 single-species and 6 mixed-species libraries and mapped the reads against 110 reference genomes of insects. We used the single-species libraries to calibrate the process of assignation of reads to species and the libraries created from species mixtures to evaluate the ability of the method to quantify the relative species abundance. Our results showed that the shotgun metagenomic method is easily able to set apart closely-related insect species, like four species of Drosophila included in the artificial libraries. However, to avoid the counting of rare misclassified reads in samples, it was necessary to use a rather stringent detection limit of 0.001, so species with a lower relative abundance are ignored. We also identified that approximately half the raw reads were informative for taxonomic purposes. Finally, using the mixed-species libraries, we showed that it was feasible to quantify with confidence the relative abundance of individual species in the mixtures.

scholarly journals A Stand-Development Approach to Oak Afforestation in the Lower Mississippi Alluvial Valley

2008 ◽  
Vol 32 (3) ◽  
pp. 120-129 ◽  
Author(s):  
Brian Roy Lockhart ◽  
Emile Gardiner ◽  
Theodor Leininger ◽  
John Stanturf
Keyword(s):  
Single Species ◽  
Wildlife Habitat ◽  
Tree Planting ◽  
Individual Species ◽  
Stand Development ◽  
Mississippi Alluvial Valley ◽  
Mixed Species ◽  
Management Options ◽  
Alluvial Valley ◽  
Lower Mississippi Alluvial Valley

Abstract Oak (Quercus spp.) afforestation in the Lower Mississippi Alluvial Valley has involved planting 1-year-old bareroot seedlings on a relatively wide spacing in single-species stands or planting light-seeded species with oaks to form mixed-species stands. In the former case, the developing single-species stands have limited future management options because they do not provide structures that favor quality wildlife habitat or quality sawtimber production. In the latter case, species mixtures are being planted with little knowledge of subsequent stand development, leading to an inability to predict future stand composition for management purposes. In this article, we present a system to determine bottomland tree planting mixtures that will create single-cohort, mixed-species stands with a component of high-quality bottomland oak. Using individual species ecological life-history characteristics, such as early height growth pattern, relative twig diameter and durability, and developmental patterns in natural stands, bottomland species are rated for their ability to provide beneficial training effects that will lead to the development of quality oak boles. Incorporating such a system to determine species value in mixtures should provide an increased number of future options to meet explicit management objectives and promote improved restoration of bottomland hardwood ecosystems.

Orchestrated Flowering and Interspecific Facilitation: Key Factors in the Maintenance of the Main Pollinator of Coexisting Threatened Species of Andean Wax Palms (Ceroxylon spp.)

2020 ◽  
Vol 105 (3) ◽  
pp. 281-299
Author(s):  
Javier Carreño-Barrera ◽  
Luis Alberto Núñez-Avellaneda ◽  
Maria José Sanín ◽  
Artur Campos D. Maia
Keyword(s):  
Conservation Status ◽  
Population Decline ◽  
Floral Biology ◽  
Fruit Production ◽  
Biological Data ◽  
Fruit Yield ◽  
Insect Species ◽  
Individual Species ◽  
Pollination Services ◽  
Flower Visiting

Solitary, dioecious, and mostly endemic to Andean cloud forests, wax palms (Ceroxylon Bonpl. ex DC. spp.) are currently under worrisome conservation status. The establishment of management plans for their dwindling populations rely on detailed biological data, including their reproductive ecology. As in the case of numerous other Neotropical palm taxa, small beetles are assumed to be selective pollinators of wax palms, but their identity and relevance in successful fruit yield were unknown. During three consecutive reproductive seasons we collected data on population phenology and reproductive and floral biology of three syntopic species of wax palms native to the Colombian Andes. We also determined the composition of the associated flower-visiting entomofauna, quantifying the extent of the role of individual species as effective pollinators through standardized value indexes that take into consideration abundance, constancy, and pollen transport efficiency. The studied populations of C. parvifrons (Engel) H. Wendl., C. ventricosum Burret, and C. vogelianum (Engel) H. Wendl. exhibit seasonal reproductive cycles with marked temporal patterns of flower and fruit production. The composition of the associated flower-visiting entomofauna, comprised by ca. 50 morphotypes, was constant across flowering seasons and differed only marginally among species. Nonetheless, a fraction of the insect species associated with pistillate inflorescences actually carried pollen, and calculated pollinator importance indexes demonstrated that one insect species alone, Mystrops rotundula Sharp, accounted for 94%–99% of the effective pollination services for all three species of wax palms. The sequential asynchronous flowering of C. parvifrons, C. ventricosum, and C. vogelianum provides an abundant and constant supply of pollen, pivotal for the maintenance of large populations of their shared pollinators, a cooperative strategy proven effective by high fruit yield rates (up to 79%). Reproductive success might be compromised for all species by the population decline of one of them, as it would tamper with the temporal orchestration of pollen offer.

From single-species advice to mixed-species management: taking the next step

2004 ◽  
Vol 61 (8) ◽  
pp. 1398-1409 ◽  
Author(s):  
Morten Vinther ◽  
Stuart A. Reeves ◽  
Kenneth R. Patterson
Keyword(s):  
North Sea ◽  
Fishery Management ◽  
Single Species ◽  
Mixed Species ◽  
The North ◽  
Recent Approach ◽  
Starting Point ◽  
The North Sea ◽  
Management Advice ◽  
Management Priorities

Abstract Fishery management advice has traditionally been given on a stock-by-stock basis. Recent problems in implementing this advice, particularly for the demersal fisheries of the North Sea, have highlighted the limitations of the approach. In the long term, it would be desirable to give advice that accounts for mixed-fishery effects, but in the short term there is a need for approaches to resolve the conflicting management advice for different species within the same fishery, and to generate catch or effort advice that accounts for the mixed-species nature of the fishery. This paper documents a recent approach used to address these problems. The approach takes the single-species advice for each species in the fishery as a starting point, then attempts to resolve it into consistent catch or effort advice using fleet-disaggregated catch forecasts in combination with explicitly stated management priorities for each stock. Results are presented for the groundfish fisheries of the North Sea, and these show that the development of such approaches will also require development of the ways in which catch data are collected and compiled.

scholarly journals Trace amines inhibit insect odorant receptor function through antagonism of the co-receptor subunit

F1000Research ◽  
2014 ◽  
Vol 3 ◽  
pp. 84 ◽  
Author(s):  
Sisi Chen ◽  
Charles W. Luetje
Keyword(s):  
Odorant Receptor ◽  
Olfactory Receptors ◽  
Single Species ◽  
Insect Species ◽  
Receptor Subunit ◽  
Trace Amines ◽  
Vector Mosquito ◽  
Exogenous Compounds ◽  
Potent Antagonist ◽  
High Degree

Many insect behaviors are driven by olfaction, making insect olfactory receptors (ORs) appealing targets for insect control.  Insect ORs are odorant-gated ion channels, with each receptor thought to be composed of a representative from a large, variable family of odorant binding subunits and a highly conserved co-receptor subunit (Orco), assembled in an unknown stoichiometry.  Synthetic Orco directed agonists and antagonists have recently been identified.  Several Orco antagonists have been shown to act via an allosteric mechanism to inhibit OR activation by odorants.  The high degree of conservation of Orco across insect species results in Orco antagonists having broad activity at ORs from a variety of insect species and suggests that the binding site for Orco ligands may serve as a modulatory site for compounds endogenous to insects or may be a target of exogenous compounds, such as those produced by plants.  To test this idea, we screened a series of biogenic and trace amines, identifying several as Orco antagonists.  Of particular interest were tryptamine, a plant-produced amine, and tyramine, an amine endogenous to the insect nervous system.  Tryptamine was found to be a potent antagonist of Orco, able to block Orco activation by an Orco agonist and to allosterically inhibit activation of ORs by odorants.  Tyramine had effects similar to those of tryptamine, but was less potent.  Importantly, both tryptamine and tyramine displayed broad activity, inhibiting odorant activation of ORs of species from three different insect orders (Diptera, Lepidoptera and Coleoptera), as well as odorant activation of six diverse ORs from a single species (the human malaria vector mosquito, Anopheles gambiae).  Our results suggest that endogenous and exogenous natural compounds serve as Orco ligands modulating insect olfaction and that Orco can be an important target for the development of novel insect repellants.

scholarly journals Decline in New Zealand's freshwater fish fauna: Effect of land use

2020 ◽  
Author(s):  
Michael Joy ◽  
KJ Foote ◽  
P McNie ◽  
M Piria
Keyword(s):  
New Zealand ◽  
Land Cover ◽  
Freshwater Fish ◽  
Native Species ◽  
Species Abundance ◽  
Fish Fauna ◽  
Fish Distribution ◽  
Individual Species ◽  
Freshwater Fish Fauna ◽  
Over Time

© 2019 CSIRO. The number of New Zealand's freshwater fish listed as threatened has increased since 1992 when the first New Zealand threat classification system list was compiled. In this study, temporal and land cover-related trends were analysed for data on freshwater fish distribution, comprising more than 20 000 records for the 47 years from January 1970 to January 2017 from the New Zealand Freshwater Fish Database. The analysis included individual species abundance and distribution trends, as well as an index of fish community integrity, namely the Index of Biotic Integrity (IBI). Of the 25 fish species that met the requirements for analysis to determine changes in the proportion of sites they occupied over time, 76% had negative trends (indicating declining occurrence). Of the 20 native species analysed for the proportion of sites occupied over time, 75% had negative trends; 65% of these were significant declines and more species were in decline at pasture sites than natural cover sites. The average IBI score also declined over the time period and, when analysed separately, the major land cover types revealed that the IBI declined at pasture catchment sites but not at sites with natural vegetation catchments.

scholarly journals Spatial Distribution of Insect Diversity in Selected Locations within Forestry Research Institute of Nigeria, Ibadan, Nigeria

2021 ◽  
Vol 25 (7) ◽  
pp. 1249-1255
Author(s):  
O.A. Aina-Oduntan ◽  
Q.A. Onilude ◽  
J.A. George-Onaho ◽  
A.I. Woghiren ◽  
O.R. Jeminiwa
Keyword(s):  
Species Diversity ◽  
Relative Abundance ◽  
Habitat Modification ◽  
Insect Species ◽  
Line Transect ◽  
Microsoft Excel ◽  
Forestry Research ◽  
Significant Difference ◽  
Ibadan Nigeria ◽  
Research Institute

With the increase in the rate of tree removal and construction of buildings within the Forestry Research Institute of Nigeria premises, there has been concomitant rise in habitat modification. These changes in habitat composition affect the insect population. This study therefore investigated the insect species diversity and abundance within some selected locations within FRIN with the view to determining different insect species available in FRIN premises. Sweep nets were used to trap the insects along a predetermined line transect. Data were analyzed using Microsoft Excel 2007 and Paleontological Statistics were used for the data analysis. Descriptive statistics, one-way analysis of variance (ANOVA) and species diversity and composition were all assessed. A total number of 1073 individual insects belonging to 6 orders, 27 families and 34 species were recorded across the three locations. Out of this, Order Lepidoptera had the highest relative abundance (53%), followed by Coleoptera (22%), then by Hymenoptera, Hemiptera, Heteroptera and Diptera with 10%, 9%, 4% and 2% relative abundance respectively. The result of ANOVA showed that there was no significant difference in species composition/richness across the locations at probability level of 5%. The insect species diversity, evenness and richness also varied across the locations. This study therefore, brings to the fore the diversity and abundance of insects within FRIN premises and highlighted the need for a more intensive study by the entomology section and for sustainable actions to be taken in conserving beneficial rare species while, managing the abundant pestiferous ones.

scholarly journals In vitrocommunity synergy between bacterial soil isolates can be facilitated by pH stabilisation of the environment

2018 ◽  
Author(s):  
Jakob Herschend ◽  
Klaus Koren ◽  
Henriette L. Røder ◽  
Asker Brejnrod ◽  
Michael Kühl ◽  
...  
Keyword(s):  
Metabolic Activity ◽  
Local Environment ◽  
Single Species ◽  
Species Interaction ◽  
Individual Species ◽  
Community Members ◽  
Community Interactions ◽  
Community Growth ◽  
Over Time

AbstractComposition and development of naturally occurring microbial communities is defined by a complex interplay between the community and the surrounding environment and by interactions between community members. Intriguingly, these interactions can in some cases cause community synergies where the community is able to outperform it single species constituents. However, the underlying mechanisms driving community interactions are often unknown and difficult to identify due to high community complexity. Here we show how pH stabilisation of the environment through the metabolic activity of specific community members acts as a positive inter-species interaction drivingin vitrocommunity synergy in a model consortium of four co-isolated soil bacteria:Microbacterium oxydans,Xanthomonas retroflexus,Stenotrophomonas rhizophilaandPaenibacillus amylolyticus. Using micro-sensor pH measurements to show how individual species change the local pH micro-environment, and how co-cultivation leads to a stabilised pH regime over time. Specifically,in vitroacid production fromPaenibacillus amylolyticusand alkali production primarily fromXanthomonas retroflexuslead to an overall pH stabilisation of the local environment over time, which in turn resulted in enhanced community growth. This specific type of interspecies interaction was found to be highly dependent on media type and media concentration, however similar pH drift from the individual species could be observed across media variants.ImportanceWe show thatin vitrometabolic activity of individual members of a synthetic, co- isolated model community presenting community synergistic growth arises through the inter-species interaction of pH stabilization of the community micro-environment. The observed inter-species interaction is highly media specific and most pronounced under high nutrient availability. This adds to the growing diversity of identified community interactions leading to enhanced community growth.

scholarly journals Dissecting individual pathogen-commensal interactions within a complex gut microbiota community

2020 ◽  
Author(s):  
Jack Hassall ◽  
Meera Unnikrishnan
Keyword(s):  
Gut Microbiota ◽  
Single Species ◽  
Species Level ◽  
Commensal Bacteria ◽  
Individual Species ◽  
Community Responses ◽  
Bacterial Interactions ◽  
Gut Pathogen ◽  
Over Time

AbstractInteractions of commensal bacteria within the gut microbiota and with invading pathogens are critical in determining the outcome of an infection. While murine studies have been valuable, we lack in vitro tools to monitor community responses to pathogens at a single-species level. We have developed a multi-species community of nine representative gut species cultured together as a mixed biofilm and tracked numbers of individual species over time using a qPCR-based approach. Introduction of the major nosocomial gut pathogen, Clostridiodes difficile, to this community resulted in increased adhesion of commensals and inhibition of C. difficile multiplication. Interestingly, we observed an increase in individual Bacteroides species accompanying the inhibition of C. difficile. Furthermore, Bacteroides dorei reduced C. difficile growth within biofilms, suggesting a role for Bacteroides spp in prevention of C. difficile colonisation. We report here an in vitro tool with excellent applications for investigating bacterial interactions within a complex community.

Harvesting at the Community Level

2020 ◽  
pp. 205-228
Author(s):  
Michael J. Fogarty ◽  
Jeremy S. Collie
Keyword(s):  
Single Species ◽  
Economic Incentives ◽  
Unintended Consequences ◽  
Community Context ◽  
Reference Points ◽  
Individual Species ◽  
Biological Interactions ◽  
Predator Prey ◽  
The Right ◽  
Technical Solutions

Most fisheries are not directed at individual species alone. Rather, in many instances, species within a community are caught together and are also part of competitive networks and food webs. Species that are caught together are subject to technical interactions. Species that compete or are connected through predator–prey interactions (or other types of interactions) are subject to biological interactions. Ignoring either of these forms of interaction in management can lead to unintended consequences. Technical solutions can help to avoid some species while targeting others, but a comprehensive solution requires creating the right economic incentives and some incidental catch is still inevitable. Accounting for trophic interactions means that biological reference points depend on the abundance of other taxa. Single-species approaches are invalid in a multispecies or community context where biological interactions are important. Technical interactions can make it impossible to achieve target exploitation rates even if biological interactions are relatively unimportant.

scholarly journals Mixed community biofilms and microbially influenced corrosion

2018 ◽  
Vol 39 (3) ◽  
pp. 152 ◽  
Author(s):  
Enrico Marsili ◽  
Staffan Kjelleberg ◽  
Scott A Rice
Keyword(s):  
Single Species ◽  
Environmental Safety ◽  
Corrosion Process ◽  
Metal Corrosion ◽  
Mixed Species ◽  
Short Article ◽  
Microbial Biofilms ◽  
Microbially Influenced Corrosion ◽  
Biochemical Mechanisms ◽  
Mixed Community

Metals are used in most marine infrastructures for energy extraction and production. Metal corrosion is a serious concern, due to the environmental, safety, and replacement costs associated with it. Microbially influenced corrosion (MIC) contributes to the overall corrosion process, through several chemical, electrochemical and biochemical mechanisms, particularly in the presence of microbial biofilms. In this short article, we discuss briefly recent advances in MIC research, comparing corrosion in single species and mixed species biofilms, and outline possible strategies for biofilm and corrosion control.

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