scholarly journals New Insights Into Nematode DNA-metabarcoding as Revealed by the Characterization of Artificial and Spiked Nematode Communities

Diversity ◽  
2019 ◽  
Vol 11 (4) ◽  
pp. 52 ◽  
Author(s):  
Lieven Waeyenberge ◽  
Nancy de Sutter ◽  
Nicole Viaene ◽  
Annelies Haegeman
Keyword(s):  
Species Richness ◽  
18S Rrna ◽  
Nematode Species ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Soil Nematode ◽  
Mock Community ◽  
Nematode Communities ◽  
Dna Metabarcoding ◽  
Soil Nematode Communities

Nematodes are ideal biological indicators to monitor soil biodiversity and ecosystem functioning. For this reason, they have been receiving increasing attention from a broad range of scientists. The main method to characterize soil nematode communities until at least genus level is still based on microscopic observations of nematode morphology. Such an approach is time-consuming, labor-intensive, and requires specialized personnel. The first studies on the potential use of DNA-metabarcoding to characterize nematode communities showed some shortcomings: under- or overestimation of species richness caused by failure to detect a number of nematode species or caused by intraspecific sequence variants increasing the number of OTUs (operational taxonomic units) or ‘molecular’ species, and flaws in quantification. We set up experiments to optimize this metabarcoding approach. Our results provided new insights such as the drastic effect of different DNA-extraction methods on nematode species richness due to variation in lysis efficacy. Our newly designed primer set (18S rRNA gene, V4-V5 region) showed in silico an improved taxonomic coverage compared with a published primer set (18S rRNA gene, V6-V8 region). However, results of DNA-metabarcoding with the new primer set showed less taxonomic coverage, and more non-nematode reads. Thus, the new primer set might be more suitable for whole soil faunal analysis. Species-specific correction factors calculated from a mock community with equal amounts of different nematode species were applied on another mock community with different amounts of the same nematode species and on a biological sample spiked with four selected nematode species. Results showed an improved molecular quantification. In conclusion, DNA-metabarcoding of soil nematode communities is useful for monitoring shifts in nematode composition but the technique still needs further optimization to enhance its precision.

scholarly journals Application of PCR-DGGE method for identification of nematode communities in pepper growing soil

2016 ◽  
Vol 7 (1) ◽  
pp. 9-14
Author(s):  
Duong Duc Hieu
Keyword(s):  
Maximum Likelihood ◽  
Community Sample ◽  
Nematode Species ◽  
Viet Nam ◽  
Soil Nematode ◽  
Nematode Communities ◽  
Maximum Likelihood Tree ◽  
Relationship Of ◽  
First Time ◽  
Soil Nematode Communities

Soil nematodes play an important role in indication for assessing soil environments and ecosystems. Previous studies of nematode community analyses based on molecular identification have shown to be useful for assessing soil environments. Here we applied PCR-DGGE method for molecular analysisoffive soil nematode communities (designed as S1 to S5) collected from four provinces in Southeastern Vietnam (Binh Duong, Ba Ria Vung Tau, Binh Phuoc and Dong Nai) based on SSU gene. By sequencing DNA bands derived from S5 community sample, our data show 15 species containing soil nematode, other nematode and non-nematode (fungi) species. Genus Meloidogyne was found as abundant one. The genetic relationship of soil nematode species in S5 community were determined by Maximum Likelihood tree re-construction based on SSU gene. This molecular approach is applied for the first time in Vietnam for identification of soil nematode communities. Tuyến trùng đất đóng vai trò chỉ thị quan trọng trong công tác đánh giá môi trường và hệ sinh thái đất. Các nghiên cứu trước đây đã cho thấy lợi ích của việc phân tích cộng đồng tuyến trùng đất bằng định danh sinh học phân tử đối với việc đánh giá môi trường đất. Ở đây, chúng tôi ứng dụng phương pháp PCR-DGGE dựa trên gene SSU để phân tích năm (ký hiệu từ S1 đến S5) cộng đồng tuyến trùng đất thuộc các vùng trồng chuyên canh cây hồ tiêu ở miền nam Việt Nam (Bình Dương, Bà Rịa Vũng Tàu, Bình Phước và Đồng Nai). Bằng cách giải trình tự các vạch của mẫu tuyến trùng S5, kết quả cho thấy cộng đồng tuyến trùng này có 15 loài gồm nhóm tuyến trùng đất, nhóm các loại tuyến trùng khác và nhóm không phải tuyến trùng (nấm) và trong đó Meloidogyne là giống ưu thế. Mối quan hệ di truyền của các các loài tuyến trùng đất thuộc cộng đồng S5 được xác định bằng việc thiết lập cây phát sinh loài Maximum Likelihood dựa trên gene SSU. Đây là nghiên cứu đầu tiên ở Việt Nam sử dụng kỹ thuật PCR-DGGE để phân tích các cộng đồng tuyến trùng đất trồng hồ tiêu.

scholarly journals Preliminary analysis of New Zealand scampi (Metanephrops challengeri) diet using metabarcoding

2018 ◽  
Author(s):  
Aimee L van der Reis ◽  
Olivier Laroche ◽  
Andrew G Jeffs ◽  
Shane D Lavery
Keyword(s):  
New Zealand ◽  
Preliminary Analysis ◽  
18S Rrna ◽  
18S Rrna Gene ◽  
Coi Gene ◽  
Taxonomic Resolution ◽  
Gut Contents ◽  
Rrna Gene ◽  
Diverse Range ◽  
Dna Metabarcoding

Deep sea lobsters are highly valued for seafood and provide the basis of important commercial fisheries in many parts of the world. Despite their economic significance, relatively little is known about their natural diets. Microscopic analyses of foregut content in some species have suffered from low taxonomic resolution, with many of the dietary items difficult to reliably identify as their tissue is easily digested. DNA metabarcoding has the potential to provide greater taxonomic resolution of the diet of the New Zealand scampi (Metanephrops challengeri) through the identification of gut contents, but a number of methodological concerns need to be overcome first to ensure optimum DNA metabarcoding results. In this study, a range of methodological parameters were tested to determine the optimum protocols for DNA metabarcoding, and provide a first view of M. challengeri diet. Several PCR protocols were tested, using two universal primer pairs targeting the 18S rRNA and COI genes, on DNA extracted from both frozen and ethanol preserved samples for both foregut and hindgut digesta. The selection of appropriate DNA polymerases, buffers and methods for reducing PCR inhibitors (including the use of BSA) were found to be critical. Amplification from frozen or ethanol preserved gut contents appeared similarly dependable, but metabarcoding outcomes indicated that the ethanol samples produced better results from the COI gene. The COI gene was found to be more effective than 18S rRNA gene for identifying large eukaryotic taxa from the digesta, however, it was less successfully amplified. The 18S rRNA gene was more easily amplified, but identified mostly smaller marine organisms such as plankton and parasites. This preliminary analysis of the diet of M. challengeri identified a range of species (13,541 reads identified as diet), which included the ghost shark (Hydrolagus novaezealandiae), silver warehou (Seriolella punctate), tall sea pen (Funiculina quadrangularis) and the salp (Ihlea racovitza), suggesting that they have a varied diet, with a high reliance on scavenging a diverse range of pelagic and benthic species from the seafloor.

scholarly journals Changes in Plant Species Richness Induce Functional Shifts in Soil Nematode Communities in Experimental Grassland

PLoS ONE ◽  
2011 ◽  
Vol 6 (9) ◽  
pp. e24087 ◽  
Author(s):  
Nico Eisenhauer ◽  
Varvara D. Migunova ◽  
Michael Ackermann ◽  
Liliane Ruess ◽  
Stefan Scheu
Keyword(s):  
Species Richness ◽  
Plant Species ◽  
Plant Species Richness ◽  
Soil Nematode ◽  
Nematode Communities ◽  
Soil Nematode Communities

scholarly journals A DNA metabarcoding approach for recovering plankton communities from archived samples fixed in formalin

PLoS ONE ◽  
2021 ◽  
Vol 16 (2) ◽  
pp. e0245936
Author(s):  
Takuhei Shiozaki ◽  
Fumihiro Itoh ◽  
Yuu Hirose ◽  
Jonaotaro Onodera ◽  
Akira Kuwata ◽  
...  
Keyword(s):  
Community Structure ◽  
18S Rrna ◽  
18S Rrna Gene ◽  
Formalin Fixation ◽  
Plankton Sample ◽  
Rrna Gene ◽  
Dna Metabarcoding ◽  
Plankton Diversity ◽  
The Impact ◽  
Formalin Fixed

Plankton samples have been routinely collected and preserved in formalin in many laboratories and museums for more than 100 years. Recently, attention has turned to use DNA information from formalin-fixed samples to examine changes in plankton diversity over time. However, no molecular ecological studies have evaluated the impact of formalin fixation on the genetic composition of the plankton community structure. Here, we developed a method for extracting DNA from archived formalin-preserved plankton samples to determine their community structure by a DNA metabarcoding approach. We found that a lysis solution consisting of borate-NaOH buffer (pH 11) with SDS and proteinase K effectively cleaved the cross-link formed by formalin fixation. DNA was extracted from samples preserved for decades in formalin, and the diatom community of the extracted DNA was in good agreement with the microscopy analysis. Furthermore, we stored a plankton sample for 1.5 years and demonstrated that 18S rRNA gene community structures did not change significantly from non-formalin-fixed, time-zero samples. These results indicate that our method can be used to describe the original community structure of plankton archived in formalin for years. Our approach will be useful for examining the long-term variation of plankton diversity by metabarcoding analysis of 18S rRNA gene community structure.

scholarly journals Characterization of soil nematode communities in three cropping systems through morphological and DNA metabarcoding approaches

2018 ◽  
Vol 8 (1) ◽  
Author(s):  
Amy M. Treonis ◽  
Samantha K. Unangst ◽  
Ryan M. Kepler ◽  
Jeffrey S. Buyer ◽  
Michel A. Cavigelli ◽  
...  
Keyword(s):  
Cropping Systems ◽  
Soil Nematode ◽  
Nematode Communities ◽  
Dna Metabarcoding ◽  
Soil Nematode Communities

Plant species richness sustains higher trophic levels of soil nematode communities after consecutive environmental perturbations

Oecologia ◽  
2017 ◽  
Vol 184 (3) ◽  
pp. 715-728 ◽  
Author(s):  
Simone Cesarz ◽  
Marcel Ciobanu ◽  
Alexandra J. Wright ◽  
Anne Ebeling ◽  
Anja Vogel ◽  
...  
Keyword(s):  
Species Richness ◽  
Plant Species ◽  
Plant Species Richness ◽  
Trophic Levels ◽  
Soil Nematode ◽  
Nematode Communities ◽  
Environmental Perturbations ◽  
Soil Nematode Communities

scholarly journals Preliminary analysis of New Zealand scampi (Metanephrops challengeri) diet using metabarcoding

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5641 ◽  
Author(s):  
Aimee L. van der Reis ◽  
Olivier Laroche ◽  
Andrew G. Jeffs ◽  
Shane D. Lavery
Keyword(s):  
New Zealand ◽  
Preliminary Analysis ◽  
18S Rrna ◽  
18S Rrna Gene ◽  
Coi Gene ◽  
Taxonomic Resolution ◽  
Gut Contents ◽  
Rrna Gene ◽  
Diverse Range ◽  
Dna Metabarcoding

Deep sea lobsters are highly valued for seafood and provide the basis of important commercial fisheries in many parts of the world. Despite their economic significance, relatively little is known about their natural diets. Microscopic analyses of foregut content in some species have suffered from low taxonomic resolution, with many of the dietary items difficult to reliably identify as their tissue is easily digested. DNA metabarcoding has the potential to provide greater taxonomic resolution of the diet of the New Zealand scampi (Metanephrops challengeri) through the identification of gut contents, but a number of methodological concerns need to be overcome first to ensure optimum DNA metabarcoding results. In this study, a range of methodological parameters were tested to determine the optimum protocols for DNA metabarcoding, and provide a first view ofM.challengeridiet. Several PCR protocols were tested, using two universal primer pairs targeting the 18S rRNA and COI genes, on DNA extracted from both frozen and ethanol preserved samples for both foregut and hindgut digesta. The selection of appropriate DNA polymerases, buffers and methods for reducing PCR inhibitors (including the use of BSA) were found to be critical. Amplification from frozen or ethanol preserved gut contents appeared similarly dependable. The COI gene was found to be more effective than 18S rRNA gene for identifying large eukaryotic taxa from the digesta; however, it was less successfully amplified. The 18S rRNA gene was more easily amplified, but identified mostly smaller marine organisms such as plankton and parasites. This preliminary analysis of the diet ofM.challengeriidentified a range of species (13,541 reads identified as diet), which included the ghost shark (Hydrolagus novaezealandiae), silver warehou (Seriolella punctata), tall sea pen (Funiculina quadrangularis) and the salp (Ihlea racovitzai), suggesting that they have a varied diet, with a high reliance on scavenging a diverse range of pelagic and benthic species from the seafloor.

Survey of nematodes associated with terrestrial slugs in Norway

2015 ◽  
Vol 90 (5) ◽  
pp. 583-587 ◽  
Author(s):  
J.L. Ross ◽  
E.S. Ivanova ◽  
B.A. Hatteland ◽  
M.B. Brurberg ◽  
S. Haukeland
Keyword(s):  
Mitochondrial Dna ◽  
18S Rrna ◽  
Morphological Analysis ◽  
Nematode Species ◽  
First Record ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Morphological Examination ◽  
Nematode Parasites ◽  
First Time

AbstractA survey of nematodes associated with terrestrial slugs was conducted for the first time in Norway. A total of 611 terrestrial slugs were collected from 32 sample sites. Slugs were identified by means of morphological examination, dissection of genitalia and molecular analysis using mitochondrial DNA. Twelve slug species were identified, representing four different slug families. Internal nematodes were identified by means of morphological analysis and the sequencing of the 18S rRNA gene. Of the sample sites studied, 62.5% were found to be positive for nematode parasites, with 18.7% of all slugs discovered being infected. Five nematode species were identified in this study:Alloionema appendiculatum,Agfa flexilis,Angiostoma limacis,Angiostomasp. andPhasmarhabditis hermaphrodita.Of these species, only one nematode was previously undescribed (Angiostomasp.). This is the first record of the presence ofA. appendiculatum,A. flexilis andA. limacisin Norway.

scholarly journals Preliminary analysis of New Zealand scampi (Metanephrops challengeri) diet using metabarcoding

2018 ◽  
Author(s):  
Aimee L van der Reis ◽  
Olivier Laroche ◽  
Andrew G Jeffs ◽  
Shane D Lavery
Keyword(s):  
New Zealand ◽  
Preliminary Analysis ◽  
18S Rrna ◽  
18S Rrna Gene ◽  
Coi Gene ◽  
Taxonomic Resolution ◽  
Gut Contents ◽  
Rrna Gene ◽  
Diverse Range ◽  
Dna Metabarcoding

Deep sea lobsters are highly valued for seafood and provide the basis of important commercial fisheries in many parts of the world. Despite their economic significance, relatively little is known about their natural diets. Microscopic analyses of foregut content in some species have suffered from low taxonomic resolution, with many of the dietary items difficult to reliably identify as their tissue is easily digested. DNA metabarcoding has the potential to provide greater taxonomic resolution of foregut and hindgut contents of the New Zealand (NZ) scampi (Metanephrops challengeri), but a number of methodological concerns need to first be overcome to ensure optimum DNA metabarcoding results. In this study, a range of methodological parameters were trialled to determine the optimum protocols for DNA metabarcoding, and provide a first view of the NZ scampi diet. Several PCR protocols were trialled, using two universal primer pairs targeting the 18S rRNA and COI genes, on DNA extracted from frozen and ethanol preserved samples of both foregut and hindgut digesta. The selection of appropriate DNA polymerases, buffers and methods for reducing PCR inhibitors (including use of BSA) were found to be critical. Amplification from frozen or ethanol preserved gut contents appeared similarly dependable, but metabarcoding results showed that ethanol samples resulted in better results from the COI gene. The COI gene was found to be more effective than 18S rRNA gene for identifying large eukaryotic taxa from the digesta, however, it was less successfully amplified. The 18S rRNA gene was more easily amplified, but identified mostly smaller marine organisms such as plankton and parasites. This preliminary analysis of the diet of the NZ scampi identified a range of species, which included the ghost shark (Hydrolagus novaezealandiae), silver warehou (Seriolella punctate), tall sea pen (Funiculina quadrangularis ) and salp (Ihlea racovitza), suggesting that they have a varied diet, with a high reliance on scavenging a diverse range of pelagic and benthic species from the seafloor.

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