scholarly journals Establishing arthropod community composition using metabarcoding: Surprising inconsistencies between soil samples and preservative ethanol and homogenate from Malaise trap catches

2019 ◽  
Vol 19 (6) ◽  
pp. 1516-1530 ◽  
Author(s):  
Daniel Marquina ◽  
Rodrigo Esparza‐Salas ◽  
Tomas Roslin ◽  
Fredrik Ronquist
Keyword(s):  
Community Composition ◽  
Soil Samples ◽  
Arthropod Community ◽  
Malaise Trap ◽  
Trap Catches

scholarly journals Establishing insect community composition using metabarcoding of soil samples, and preservative ethanol and homogenate from Malaise trap catches: surprising inconsistencies between methods

2019 ◽  
Author(s):  
Daniel Marquina ◽  
Rodrigo Esparza-Salas ◽  
Tomas Roslin ◽  
Fredrik Ronquist
Keyword(s):  
Community Composition ◽  
Sampling Methods ◽  
Soil Samples ◽  
Malaise Trap ◽  
Insect Community ◽  
Insect Communities ◽  
Target Dna ◽  
Dna Metabarcoding ◽  
Alternative Approaches ◽  
Trap Catches

AbstractDNA metabarcoding allows the analysis of insect communities faster and more efficiently than ever before. However, metabarcoding can be conducted through several alternative approaches, and the consistency of results across methods has rarely been studied. We compare the results obtained by DNA metabarcoding of the same communities using two different markers – COI and 16S – and three different sampling methods – homogenized Malaise trap samples (homogenate), preservative ethanol from the same samples, and soil samples. Our results indicate that COI and 16S offer partly complementary information on Malaise trap samples, with each marker detecting a significant number of species not detected by the other. Different sampling methods offer highly divergent estimates of community composition. The community recovered from preservative ethanol of Malaise trap samples is quite distinct from that recovered from homogenate. Small and weakly sclerotized insects tend to be overrepresented in ethanol, with some exceptions that could be related to taxon-specific traits. For soil samples, highly degenerate COI primers pick up large amounts of non-target DNA and only 16S provides adequate analyses of insect diversity. However, even with 16S, very little overlap in MOTU content was found between the trap and the soil samples. Our results demonstrate that no metabarcoding approach is all-comprehensive in itself. For instance, DNA extraction from preservative ethanol is not a valid replacement for destructive bulk extraction but a complement. In future metabarcoding studies, both should ideally be used together to achieve comprehensive representation of the target community.

THE EFFECT OF SOD TYPE ON THE OCCURRENCE OF GROUND BEETLES (COLEOPTERA: CARABIDAE) IN A PEST MANAGEMENT APPLE ORCHARD

1984 ◽  
Vol 116 (2) ◽  
pp. 165-171 ◽  
Author(s):  
N. J. Holliday ◽  
E. A. C. Hagley
Keyword(s):  
Pest Management ◽  
Pitfall Trap ◽  
Common Species ◽  
Ground Beetles ◽  
Apple Orchard ◽  
Soil Samples ◽  
Soil Sampling ◽  
Pitfall Trapping ◽  
Before And After ◽  
Trap Catches

AbstractThe effects on carabids of natural, fescue, and rye sod types and of tillage were investigated in a pest management apple orchard. Carabids were sampled before and after the treatments by pitfall trapping and by two types of soil sampling. There were no significant effects of sod type on pitfall trap catches; however the abundance of all common species in soil samples was significantly affected by sod types. Usually in soil samples carabids were most abundant in natural sod and least abundant in tilled plots; numbers were intermediate in fescue and rye. Sod type did not affect structure or diversity of the carabid fauna.

scholarly journals Capões como Ilhas para Artrópodes no Pantanal

2013 ◽  
Vol 6 (3) ◽  
pp. 173-177 ◽  
Author(s):  
Rodrigo Aranda
Keyword(s):  
Leaf Litter ◽  
Community Composition ◽  
Riparian Vegetation ◽  
Flood Pulse ◽  
Soil Arthropods ◽  
Arthropod Community ◽  
Plastic Bags

A configuração do habitat é um dos fatores que pode influenciar a distribuição dos organismos. O pantanal por apresentar mosaico natural de formações se enquadra para testar tais afirmações. O presente estudo teve como objetivo avaliar se a distância e o tamanho de capões afetam a composição da comunidade de artrópodes testando a hipótese de que quanto maior e mais próximo o capão da mata ciliar, maior sua diversidade. Foram amostradas seis parcelas de 30 cm² em nove capões onde a serrapilheira e o solo foram coletados, acondicionados em sacos plásticos e posteriormente triados. Houve relação entre a composição da comunidade de artrópodes em relação à distância e o tamanho indicando que o pulso de inundação do último ano afetou de forma significativa a comunidade de artrópodes de solo em capões. O acompanhamento dos processos de recolonização dos capões é sugerido. Capons as Island for Arthropods in Pantanal Abstract. The configuration of habitat is one of the factors that influence the distribution of organisms. The Pantanal by presenting mosaic natural formations fit to test such claims. The present study aimed to evaluate the distance and size of riparian capons affect the community composition of arthropods tested the hypothesis that the higher and closer to the capon of riparian vegetation, the greater its diversity. We sampled six plots of 30 cm² in nine capons where the leaf-litter and soil were collected, placed in plastic bags and later sorted. There was a relationship between the composition of arthropod community in relation to distance and size indicating that the flood pulse of the last year significantly affected the community of soil arthropods in geldings. The monitoring of the processes of recolonization of the capons is suggested.

scholarly journals Inoculation with Rhizophagus irregularis Does Not Alter Arbuscular Mycorrhizal Fungal Community Structure within the Roots of Corn, Wheat, and Soybean Crops

2020 ◽  
Vol 8 (1) ◽  
pp. 83 ◽  
Author(s):  
Sébastien Renaut ◽  
Rachid Daoud ◽  
Jacynthe Masse ◽  
Agathe Vialle ◽  
Mohamed Hijri
Keyword(s):  
Community Composition ◽  
Arbuscular Mycorrhizal ◽  
Illumina Miseq ◽  
Amplicon Sequencing ◽  
Soil Samples ◽  
Rhizophagus Irregularis ◽  
Community Diversity ◽  
Reference Sequence ◽  
Growth Stages ◽  
Arbuscular Mycorrhizal Fungal

Little is known about establishment success of the arbuscular mycorrhizal fungal (AMF) inocula and their effects on a soil-indigenous community of AMF. In this study, we assessed the effect of introducing Rhizophagus irregularis DAOM-197198 in soil under field condition on the community composition of indigenous AMF in the roots of corn (Zea mays), soybean (Glycine max), and wheat (Triticum aestivum). Three field trials were conducted with inoculated and non-inoculated plots. Four to ten roots and their rhizosphere soil samples of two growth stages for corn and wheat, and one growing stage of soybean, were collected, totalling 122 root and soil samples. Root colonization was measured microscopically, and the fungal communities were determined by paired-end Illumina MiSeq amplicon sequencing using 18S rDNA marker. After quality trimming and merging of paired ends, 6.7 million sequences could be assigned to 414 different operational taxonomic units. These could be assigned to 68 virtual taxa (VT) using the AMF reference sequence database MaarjAM. The most abundant VT corresponded to R. irregularis. The inoculation treatment did not influence the presence of R. irregularis, or AMF community diversity in roots. This seems to indicate that inoculation with R. irregularis DAOM-197198 does not change the indigenous AMF community composition, probably because it is already present in high abundance naturally.

scholarly journals Association of Microbial Community Composition and Activity with Lead, Chromium, and Hydrocarbon Contamination

2002 ◽  
Vol 68 (8) ◽  
pp. 3859-3866 ◽  
Author(s):  
W. Shi ◽  
J. Becker ◽  
M. Bischoff ◽  
R. F. Turco ◽  
A. E. Konopka
Keyword(s):  
Heavy Metals ◽  
Microbial Community ◽  
Microbial Biomass ◽  
Community Composition ◽  
Microbial Community Composition ◽  
Soil Samples ◽  
Hydrocarbon Contamination ◽  
Total Petroleum Hydrocarbons ◽  
Organic C ◽  
Microbial C

ABSTRACT Microbial community composition and activity were characterized in soil contaminated with lead (Pb), chromium (Cr), and hydrocarbons. Contaminant levels were very heterogeneous and ranged from 50 to 16,700 mg of total petroleum hydrocarbons (TPH) kg of soil−1, 3 to 3,300 mg of total Cr kg of soil−1, and 1 to 17,100 mg of Pb kg of soil−1. Microbial community compositions were estimated from the patterns of phospholipid fatty acids (PLFA); these were considerably different among the 14 soil samples. Statistical analyses suggested that the variation in PLFA was more correlated with soil hydrocarbons than with the levels of Cr and Pb. The metal sensitivity of the microbial community was determined by extracting bacteria from soil and measuring [3H]leucine incorporation as a function of metal concentration. Six soil samples collected in the spring of 1999 had IC50 values (the heavy metal concentrations giving 50% reduction of microbial activity) of approximately 2.5 mM for CrO4 2− and 0.01 mM for Pb2+. Much higher levels of Pb were required to inhibit [14C]glucose mineralization directly in soils. In microcosm experiments with these samples, microbial biomass and the ratio of microbial biomass to soil organic C were not correlated with the concentrations of hydrocarbons and heavy metals. However, microbial C respiration in samples with a higher level of hydrocarbons differed from the other soils no matter whether complex organic C (alfalfa) was added or not. The ratios of microbial C respiration to microbial biomass differed significantly among the soil samples (P < 0.05) and were relatively high in soils contaminated with hydrocarbons or heavy metals. Our results suggest that the soil microbial community was predominantly affected by hydrocarbons.

scholarly journals Malaise Trap Catches and the Crisis in Neotropical Dipterology

2005 ◽  
Vol 51 (3) ◽  
pp. 180-183 ◽  
Author(s):  
Brian V. Brown
Keyword(s):  
Malaise Trap ◽  
Trap Catches
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