Detection of Invertebrate Suppressive Soils, and Identification of a Possible Biological Control Agent for Meloidogyne Nematodes Using High Resolution Rhizosphere Microbial Community Analysis

White clover (Trifolium repens) is the key legume component of New Zealand pastoral agriculture due to the high quality feed and nitrogen inputs it provides. Invertebrate pests constrain white clover growth and this study investigated rhizosphere-associated fungal controls for two of these pests and attempts to disentangle the underpinning mechanisms. The degree of suppressiveness of 10 soils, in a latitudinal gradient down New Zealand, to added Meloidogyne hapla and Costelytra zealandica scarab larvae was measured in untreated soil. Most of the soils showed no suppressive activity against these pests but two showed activity against M. hapla and two against C. zealandica. Rhizosphere fungi responsible for pest suppressive responses were elucidated via next-generation sequencing. In the M. hapla-suppressive soils nematode-trapping Orbiliomycetes fungi were present in significantly greater abundance than non-suppressive soils and their abundance increased further with addition of M. hapla. A comparison of plant growth and the rhizosphere fungal community between untreated and irradiated soil was carried out on 5 of the 10 soils using Pyronota as the scarab larvae. Soil irradiation either: reduced (by 60–70%); increased (16×) or made no difference to white clover growth across the five soils tested, illustrating the range of microbial impacts on plant production. In one of the M. hapla suppressive soils irradiation resulted in a significant increase in nematode galling suggesting that Orbiliomycetes fungi were indeed responsible for the suppressive effect. Lack of consistent changes in soil macronutrients and pH post-irradiation suggest these were not responsible for plant or invertebrate responses. The use of next generation sequencing in controlled pot trials has allowed identification of a potential biological control organism and bioindicator for M. hapla suppression.

[1]  V. Snow,et al.  Modelling the seasonal and geographical pattern of pasture production in New Zealand , 2011 .

[2]  Robin Sen,et al.  UNITE: a database providing web-based methods for the molecular identification of ectomycorrhizal fungi. , 2005, The New phytologist.

[3]  M. Templeton,et al.  New Zealand pest management: current and future challenges , 2015 .

[4]  N. Bell,et al.  First report of Melodogyne fallax hosted by Trifolium repens (white clover): implications for pasture and crop rotations in New Zealand , 2016, Australasian Plant Disease Notes.

[5]  Jörg Römbke,et al.  Illumina metabarcoding of a soil fungal community , 2013 .

[6]  Dev T. Britto,et al.  NH4+ toxicity in higher plants: a critical review , 2002 .

[7]  M. Noonan,et al.  Serratia entomophila sp. nov. Associated with Amber Disease in the New Zealand Grass Grub Costelytra zealandica , 1988 .

[8]  H. Bouwmeester,et al.  Metabolomics in the Rhizosphere: Tapping into Belowground Chemical Communication. , 2016, Trends in plant science.

[9]  Eric P. Nawrocki,et al.  An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea , 2011, The ISME Journal.

[10]  A. Vilcinskas,et al.  Metabolites from nematophagous fungi and nematicidal natural products from fungi as an alternative for biological control. Part I: metabolites from nematophagous ascomycetes , 2015, Applied Microbiology and Biotechnology.

[11]  A. Stewart,et al.  DEVELOPMENT OF A TOMATO/ROOT KNOT NEMATODE BIOASSAY TO SCREEN BENEFICIAL MICROBES , 2009 .

[12]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[13]  C. Mercer,et al.  Evaluation of 15 Trifolium spp. and of Medicago sativa as Hosts of Four Meloidogyne spp. Found in New Zealand. , 1997, Journal of nematology.

[14]  Satoshi Yamamoto,et al.  High-Coverage ITS Primers for the DNA-Based Identification of Ascomycetes and Basidiomycetes in Environmental Samples , 2012, PloS one.

[15]  Shaun Wilson,et al.  First report , 1992 .

[16]  William A. Walters,et al.  QIIME allows analysis of high-throughput community sequencing data , 2010, Nature Methods.

[17]  P. A. A. Poof.  Tylenchida, parasites of plants and insects , 1988, Netherlands Journal of Plant Pathology.

[18]  W. M. Kain,et al.  Development of resistant pasture and methods of pasture management for grass grub (Costelytra zealandica (White)) control , 1977 .

[19]  R. East,et al.  THE EFFECT OF GRASS GRUB ON THE HERB- AGE PRODUCTION OF DIFFERENT PASTURE SPECIES IN THE PUMICE COUNTRY , 1978 .

[20]  Frédéric Mahé,et al.  Swarm: robust and fast clustering method for amplicon-based studies , 2014, PeerJ.

[21]  Renu,et al.  Evaluation of biocontrol potential of Arthrobotrys oligospora against Meloidogyne graminicola and Rhizoctonia solani in Rice (Oryza sativa L.) , 2012 .

[22]  B. Moeskops,et al.  Selective sterilisation of undisturbed soil cores by gamma irradiation: Effects on free-living nematodes, microbial community and nitrogen dynamics , 2012 .

[23]  C. Pieterse,et al.  The rhizosphere microbiome and plant health. , 2012, Trends in plant science.

[24]  R. N. Watson,et al.  Optimising the Whitehead and Hemming tray method to extract plant parasitic and other nematodes from two soils under pasture , 2001 .

[25]  R. A. Skipp,et al.  Invasion of white clover roots by fungi and other soil micro-organisms IV. Survey of root-invading fungi and nematodes in some New Zealand pastures , 1983 .

[26]  G. Shaw,et al.  Land Use , 1977, Ecology, Revised and Expanded.

[27]  M. O’Callaghan,et al.  Physicochemical properties of 50 New Zealand pasture soils: a starting point for assessing and managing soil microbial resources , 2013 .

[28]  C. C. Doncaster.  A counting dish for nematodes , 1962 .

[29]  C. Ronson,et al.  Plasmid-Located Pathogenicity Determinants of Serratia entomophila, the Causal Agent of Amber Disease of Grass Grub, Show Similarity to the Insecticidal Toxins of Photorhabdus luminescens , 2000, Journal of bacteriology.

[30]  Herdina,et al.  Development of a routine DNA-based testing service for soilborne diseases in Australia , 2008, Australasian Plant Pathology.

[31]  Angélique Bongers.  De nematoden van Nederland. , 1988 .

[32]  Martin Hartmann,et al.  Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities , 2009, Applied and Environmental Microbiology.

[33]  M. Moens,et al.  Meloidogyne species: a diverse group of novel and important plant parasites , 2009 .

[34]  I. R. Johnson,et al.  Simulating pasture growth rates in Australian and New Zealand grazing systems , 2008 .

[35]  K. Davies.  Understanding the interaction between an obligate hyperparasitic bacterium, Pasteuria penetrans and its obligate plant-parasitic nematode host, Meloidogyne spp. , 2009, Advances in parasitology.

[36]  H. Tun,et al.  An extended single‐index multiplexed 16S rRNA sequencing for microbial community analysis on MiSeq illumina platforms , 2016, Journal of basic microbiology.

[37]  M. O’Callaghan,et al.  Cost of root disease on white clover growth in New Zealand dairy pastures , 2016, Australasian Plant Pathology.

[38]  Keqin Zhang,et al.  Phylogenetics and evolution of nematode-trapping fungi (Orbiliales) estimated from nuclear and protein coding genes , 2005 .

[39]  Jiajie Zhang,et al.  PEAR: a fast and accurate Illumina Paired-End reAd mergeR , 2013, Bioinform..

[40]  Keqin Zhang,et al.  Phylogenetics and evolution of nematode-trapping fungi (Orbiliales) estimated from nuclear and protein coding genes. , 2005, Mycologia.

[41]  Jun Peng,et al.  Development of a Real-Time Fluorescence Loop-Mediated Isothermal Amplification Assay for Rapid and Quantitative Detection of Fusarium oxysporum f. sp. cubense Tropical Race 4 In Soil , 2013, PloS one.