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

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.

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

Diversity ◽

10.3390/d11040052 ◽

2019 ◽

Vol 11 (4) ◽

pp. 52 ◽

Cited By ~ 9

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.

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Influence of Asclepias syriaca on soil nematode communities

Folia Oecologica ◽

10.2478/foecol-2021-0009 ◽

2021 ◽

Vol 48 (1) ◽

pp. 73-81

Author(s):

Michaela Jakubcsiková ◽

Andrea Čerevková ◽

Marek Renčo

Keyword(s):

Nematode Species ◽

Parasitic Nematodes ◽

Soil Nematode ◽

Trophic Groups ◽

Asclepias Syriaca ◽

Nematode Communities ◽

Structure Of Communities ◽

Aphelenchus Avenae ◽

The Impact ◽

Soil Nematode Communities

Abstract The main goal of this study was to evaluate the impact of the invasive common milkweed (Asclepias syriaca L.) on soil nematode communities. The research was carried out in 2018 and 2019 in an ecosystem of permanent grassland in the basin of the Laborec River in land registries of Drahňov, a Vojany village in southeastern Slovakia. The ecosystem contained a total of 64 species of free-living and parasitic nematodes. The most prevalent trophic groups were bacterial feeders (Acrobeloides nanus), followed by plant parasites (Helicotylenchus digonicus and Pratylenchus pratensis), fungal feeders (Aphelenchus avenae), and omnivores (Eudorylaimus carteri). The number of nematode species, the composition of trophic groups and the structure of communities in areas with invasive plants were similar to those in areas with native vegetation during the two years of observation.

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Two new species of Homaloxestis Meyrick, 1910 (Lepidoptera: Lecithoceridae) from Uganda, with a checklist of the genus in the Afrotropical Region

Zootaxa ◽

10.11646/zootaxa.4658.3.10 ◽

2019 ◽

Vol 4658 (3) ◽

pp. 591-598

Author(s):

KYU-TEK PARK ◽

JUN-MO KOO ◽

WOLFRAM MEY

Keyword(s):

New Species ◽

Maximum Likelihood ◽

Female Genitalia ◽

Dr Congo ◽

Maximum Likelihood Tree ◽

Afrotropical Region ◽

Two New Species ◽

Relationship Of ◽

First Time ◽

The Relationship

Two new species of the genus Homaloxestis Meyrick, 1910 are described from Uganda, Africa: H. arcuatus sp. nov. and H. lactizonalis sp. nov. A previously known species of the genus from Uganda, H. hemigastra Meyrick, 1931 is transferred to the genus Furcalis Park as F. hemigastra (Meyrick, 1931), comb. nov. The female of F. hemigastra is reported for the first time and described and illustrated. New distributional data for H. lophophora Janse for DR Congo, Tanzania and Uganda are given, and a maximum likelihood-tree of the four COI barcoded species of Homaloxestis is provided to reconfirm the relationship of H. lophophora Janse and H. cholopis (Meyrick). Diagnosis, descriptions and illustrations of adults, male and/or female genitalia for the new species, and the venation of H. lactizonalis sp. nov. are provided. A checklist of the species of the genus Homaloxestis Meyrick in the Afrotropical region is given.

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Carbofuran effects in soil nematode communities: Using trait and taxonomic based approaches

Ecotoxicology and Environmental Safety ◽

10.1016/j.ecoenv.2011.07.015 ◽

2011 ◽

Vol 74 (7) ◽

pp. 2002-2012 ◽

Cited By ~ 22

Author(s):

Sónia Chelinho ◽

Klaus Dieter Sautter ◽

Anabela Cachada ◽

Isabel Abrantes ◽

George Brown ◽

...

Keyword(s):

Soil Nematode ◽

Nematode Communities ◽

Soil Nematode Communities

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Soil nematode communities associated with hazelnut orchards in Turkey

Journal of Entomology and Nematology ◽

10.5897/jen2014.0104 ◽

2014 ◽

Vol 6 (8) ◽

pp. 112-121 ◽

Cited By ~ 1

Author(s):

Akyazi Faruk ◽

Yildiz Senol ◽

Firat Felek Anil

Keyword(s):

Soil Nematode ◽

Nematode Communities ◽

Soil Nematode Communities

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Neotyphodium impacts on soil nematode communities: rhizosphere- and litter-mediated interactions

NZGA: Research and Practice Series ◽

10.33584/rps.13.2006.3098 ◽

2007 ◽

Vol 13 ◽

pp. 107-110

Author(s):

M. Omacini ◽

E.J. Chaneton ◽

C.M. Ghersa

Keyword(s):

Plant Traits ◽

Lolium Multiflorum ◽

Fungal Endophytes ◽

Patch Dynamics ◽

Trophic Levels ◽

Soil Nematode ◽

Patch Occupancy ◽

Nematode Communities ◽

Endophyte Infection ◽

Soil Nematode Communities

There is a growing recognition that endophyte effects on host plant traits may be propagated through food chains. We studied Neotyphodium occultans effects on soil nematode communities mediated by current and past patch occupancy by endophyteinfected Lolium multiflorum populations. A microcosm experiment was performed to evaluate whether abundance and diversity of nematodes at different trophic levels were affected by endophyte infection through rhizosphere-mediated or littermediated effects. We found that presence of endophyte-infected plants and their aerial litter both triggered a bottom-up trophic cascade enhancing the abundance of herbivorous and predaceous nematode taxa. Endophyte infection also increased overall nematode richness, mostly through changes induced at the highest trophic level in this soil food web. Our results suggest that fungal endophytes can modify the linkages between aboveand belowground community compartments, with potential consequences on plant patch dynamics. Keywords: soil food webs, Lolium multiflorum, Neotyphodium occultans, plant-soil feedback, after-life effects, indirect interactions, trophic cascades

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Effects of biological soil crusts on soil nematode communities following dune stabilization in the Tengger Desert, Northern China

Applied Soil Ecology ◽

10.1016/j.apsoil.2011.06.007 ◽

2011 ◽

Vol 49 ◽

pp. 118-124 ◽

Cited By ~ 21

Author(s):

Yanmei Liu ◽

Xinrong Li ◽

Rongliang Jia ◽

Lei Huang ◽

Yuyan Zhou ◽

...

Keyword(s):

Northern China ◽

Biological Soil Crusts ◽

Soil Nematode ◽

Tengger Desert ◽

Nematode Communities ◽

Dune Stabilization ◽

Soil Crusts ◽

The Tengger Desert ◽

Soil Nematode Communities

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Climate change and land use induce functional shifts in soil nematode communities

Oecologia ◽

10.1007/s00442-019-04560-4 ◽

2019 ◽

Vol 192 (1) ◽

pp. 281-294 ◽

Cited By ~ 1

Author(s):

Julia Siebert ◽

Marcel Ciobanu ◽

Martin Schädler ◽

Nico Eisenhauer

Keyword(s):

Climate Change ◽

Land Use ◽

Soil Nematode ◽

Nematode Communities ◽

Soil Nematode Communities

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A contribution towards the systematics of Magneuptychia Forster, 1964: Caeruleuptychia francisca (Butler, 1870), n. comb. (Lepidoptera: Nymphalidae: Satyrinae)

Tijdschrift voor Entomologie ◽

10.1163/22119434-bja10004 ◽

2020 ◽

pp. 1-11

Author(s):

Shinichi Nakahara ◽

Kaylin Kleckner ◽

Gerardo Lamas ◽

Blanca Huertas ◽

Keith R. Willmott

Keyword(s):

Maximum Likelihood ◽

Molecular Data ◽

Maximum Likelihood Analysis ◽

Maximum Likelihood Tree ◽

Likelihood Analysis ◽

First Time

We here transfer an euptychiine taxon hitherto placed in the polyphyletic genus Magneuptychia Forster, 1964, to Caeruleuptychia Forster, 1964. Caeruleuptychia francisca (Butler, 1870), n. comb. is reclassified based on a morphology-based maximum likelihood analysis, which is consistent with ongoing analyses of molecular data. Two putative synapomorphic characters are identified for the “Caeruleuptychia umbrosa clade”, one of which appears to be an unusual characteristic of euptychiine butterflies and is tested by optimizing onto the maximum likelihood tree. We also discuss the systematic placement of three additional enigmatic Caeruleuptychia species. A lectotype is designated for Euptychia francisca, and the genitalia of this species are illustrated here for the first time.

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