Use of universal primers for the 18S ribosomal RNA gene and whole soil DNAs to reveal the taxonomic structures of soil nematodes by high-throughput amplicon sequencing

Nematodes are abundant metazoans that play crucial roles in nutrient recycle in the pedosphere. Although high-throughput amplicon sequencing is a powerful tool for the taxonomic profiling of soil nematodes, polymerase chain reaction (PCR) primers for amplification of the 18S ribosomal RNA (SSU) gene and preparation of template DNAs have not been sufficiently evaluated. We investigated nematode community structure in copse soil using four nematode-specific (regions 1–4) and two universal (regions U1 and U2) primer sets for the SSU gene regions with two DNAs prepared from copse-derived mixed nematodes and whole soil. The major nematode-derived sequence variants (SVs) identified in each region was detected in both template DNAs. Order level taxonomy and feeding type of identified nematode-derived SVs were distantly related between the two DNA preparations, and the region U2 was closely related to region 4 in the non-metric multidimensional scaling (NMDS) based on Bray-Curtis dissimilarity. Thus, the universal primers for region U2 could be used to analyze soil nematode communities. We further applied this method to analyze the nematodes living in two sampling sites of a sweet potato-cultivated field, where the plants were differently growing. The structure of nematode-derived SVs from the two sites was distantly related in the principal coordinate analysis (PCoA) with weighted unifrac distances, suggesting their distinct soil environments. The resultant ecophysiological status of the nematode communities in the copse and field on the basis of feeding behavior and maturity indices was fairly consistent with those of the copse- and the cultivated house garden-derived nematodes in prior studies. These findings will be useful for the DNA metabarcoding of soil eukaryotes, including nematodes, using soil DNAs.

Freund oder Feind? — Die zwei Gesichter von Photorhabdus luminescens

Photorhabdus luminescens is an enteric bacterium with two faces: on the one hand these bacteria live in symbiosis with soil nematodes, on the other hand they are highly pathogenic for insects. The population is also phenotypically heterogeneous: one part lives in symbiosis with nematodes, the other part symbiotically interacts with plants. Cell-cell communication, inter-kingdom signaling, and other gene regulation processes are behind the complex decision of being friend or foe.

Plant-Eating Nematodes and the Key to Fighting Them

Plant roots interact with many bacteria, fungi, and microscopic organisms within the soil that can impact how well the plants grow. Some of these microscopic organisms are animals called nematodes, and they are an especially important part of the life in the soil. Nematodes can be good, bad, and neutral for plants. Some scientists called nematologists study nematodes and how to prevent the bad ones from damaging important crops, like carrots. Nematologists and other scientists partner up to help farmers manage these pests and grow healthy crops.

Eukarya biodiversity in the Thala Hills, East Antarctica

Knowledge of the biodiversity of the Thala Hills oasis (Enderby Land, East Antarctica) is very limited. Here, we integrate all information available since 1962, when the Russian ‘Molodyozhnaya’ station was established in the western part of the oasis. The published data on local eukaryote diversity (lichens, embryophytes, metazoans) include records of 90 species. Since 2008, Belarusian Antarctic Expedition researchers have worked in the eastern part of the oasis, accessible from the Belarusian station ‘Vechernyaya Mount'. This research revealed 95 species, including 44 species not recorded in the earlier published literature. The level of available information is uneven across major taxa. Lichens are the better-known group, with 51 species recorded in total, including 13 species recently recorded for the first time in the oasis. New records were also obtained for rotifers. Thala Hills biodiversity is consistent with wider patterns of Antarctic biogeography, with a high proportion of regionally endemic species (especially metazoans), the occurrence of both endemic and bipolar species of lichens and generally low numbers of cosmopolitan species (largely limited to aquatic rotifers, with the caveat that up-to-date taxonomic studies are required). The lack of data on marine macrobenthos, soil nematodes and terrestrial rotifers emphasizes the need for studies focusing on these groups.

Identifikasi Nematoda pada Lahan Kebun Raya Banua Banjarbaru, Kalimantan Selatan

This research is to identify soil nematodes in Kebun Raya Banua in the province of South Kalimantan. Soil samples were taken to a depth of 0-20 cm. Nematodes extraction were conducted using Whitehead and Hemming method. Nematodes were killed by hot formaline. Permanent slides were prepared using Seinhorst (1962) method. Identification was carried out using a microscope with up to 1000x magnification. Two genera of the Order Dorylaimida (Aporcelaimellus and Xiphinema), one genus of the Order Monochida (Iotonchus), and one genus of the order Tylenchida (Criconema) were found.

A reference of identification keys to plant-parasitic nematodes (Nematoda: Tylenchida\ Tylenchomorpha)

The present review has documented a list of keys for identifying plant-parasitic nematodes at different taxonomic levels including superfamily, family, subfamily, genus, and species. It was compiled as a current source of information to assist students and professionals in the discipline of nematology for identification of this important group of soil nematodes.

Ozonated water electrolytically generated by diamond-coated electrodes controlled phytonematodes in replanted soil

Phytonematodes cause severe yield losses in horticulture, partly because they are difficult to manage. Compact, energy-efficient generators that electrochemically produce ozonated water by utilizing diamond-coated electrodes have become available. In this study, the application of on-site generated ozonated water to inactivate soil nematodes and to mitigate nematode-mediated apple replant disease was tested. Pratylenchus penetrans was highly susceptible to dissolved ozone (LC50 0.6 mg L−1). In one greenhouse experiment, treatment of P. penetrans in soil with ozonated water (0.27 mg ozone L−1 soil) reduced subsequent invasion of the nematodes into roots by 60%. Growth of apple saplings in soil that was affected by apple replant disease (ARD) was significantly improved following a treatment with 1/10 volume ozonated water compared to the control. In a second greenhouse experiment, one-time drenching of ARD soil with ozonated water was followed by improved growth of apple plants similar to that in autoclaved soil. A second application of ozonated water did not further improve plant growth. The number of active nematodes in replanted soil that moved through a Baermann filter was significantly reduced by all tested concentrations of ozone (0.12–0.75 mg L−1 soil). A fraction of 19–36% of the nematodes survived and slightly recovered after four weeks. In conclusion, on-site generated ozonated water has potential to mitigate nematode problems in horticulture and to expand management options.

Nematodes as Biological Indicators of Soil Quality in the Agroecosystems

Soil nematodes have advantages as bio-indicators, because they have beneficial role in the food web. Nematodes associated with bacteria are probably the most studied biological indicators of soil fertility. Saprophytic nematodes act as bio-indicators of soil health because they have different beneficial ways to increase in soil functions such as in management of ecosystem; enhancement of nitrogen in soil by ingestion of nitrogen and secrete extra nitrogen as NH4, that is easily absorbable; putrefaction and by dispersion of bacteria and fungi to recently available organic residues. Therefore, nematode are beneficial in increasing soil health or plant growth by providing the nutrient through associated bacteria. So it can be evaluated that the nematodes use as biological indicators of soil fertility because of remarkable diversity and nematode contribution in many functions of the soil fertility.