Nematode soil community structure and function as a bio-indicator of soil health in fynbos and deciduous fruit orchards

Kapp, Caro (2013-03)

Thesis (MScAgric)--Stellenbosch University, 2013.

Thesis

ENGLISH ABSTRACT: Soil is a fundamental, non-renewable resource in any ecosystem. To uphold food production for increasing global human populations, it is imperative to develop ways in which to sustain healthy biological productivity and sustainability of agricultural soils. Nematodes are one of the most abundant groups of Metazoa occurring in all soils, and form an integral part of the soil food web at several trophic levels. They respond rapidly to changes within their environments, and can easily be extracted from soil, identified and characterised into functional guilds. Nematodes thus have the potential to impart insight into the condition of the soil food web. This study aims to establish whether nematodes will be suitable bio-indicators of soil health for the deciduous fruit industry in the Western Cape. Three different objectives have been set to determine the practical use of nematode community structures as a tool for the measurement of soil health. The objectives include describing the nematode community structure, biodiversity and functionality within Fynbos soils; the characterization of organic and conventional orchards; and the differences in nematode soil communities in differently managed soils in an apple orchard. The number of nematodes in each soil sample was quantified and identified to family level. The nematode biodiversity and functionality for each site was determined by evaluating the nematode food webs for trophic group distribution, as enumerated by the Maturity Index (MI), the Enrichment Index (EI), the Structure Index (SI), the Basal Index (BI) and the Channel Index (CI), based on the weighted abundance of coloniser-persister guilds. The functional guild analysis of Fynbos samples indicated that the enrichment and the structure of any given sample were not bound to a certain area, but it was representative of each of the four quadrats within the faunal analysis. Different geographic areas were found to differ in nematode diversity and functionality, which was mainly associated with dominant plant families and species (such as strong associations between Fynbos families Fabaceae, Solanaceae and Celestraceae with the nematode family Pratylenchidae). The most abundant nematode families present in the Fynbos were Tylenchidae, which are plant-feeding nematodes, and Cephalobidae which are bacterial-feeding nematodes. Despite Tylenchidae and Cephalobidae both having coloniser-persister values (cp-values) of two, they are split up into different feeding types. Cp-2 nematodes are tolerant to disturbances, and occur in all environments. Only one omnivorous family, the Dorylaimida, was identified in Fynbos samples. The average MI value for Fynbos was found to be very low, with a mean value of 1.26. The value obtained indicated the presence of taxa with tolerance to disturbance, which, in turn, indicated the presence of a disturbed soil, in general. The number of plant-parasitic nematodes within the Fynbos soils was low, which was supported by the low plant-parasitic index (PPI) of 0.85. The diversity, richness and evenness values were low, indicating low nematode diversity, but a distribution of abundances amongst the families. The average Hill’s N0 index value was 8.0, indicating that, in general, eight nematode families would have been present in a Fynbos soil sample. A study was done to determine the biodiversity and the functionality of the nematodes associated with deciduous fruit orchards that were conventionally, or organically, managed. Herbivores were dominant in all the orchards. The organic apple orchard had the lowest numbers of herbivores and fungivores, with the highest number of carnivores. When comparing organic and conventional apricot orchards, higher numbers of plant-parasitic nematodes were found in the organic orchard. Criconematidae occurred in higher numbers in conventional apricot orchard soil. When comparing organic apricots and apples, higher numbers of Criconematidae occurred within the organic apple soil. Overall, higher levels of plant-parasitic nematodes occurred in the organic apricot orchard. The MI indicated that all orchard soils had values below 1.5, indicating disturbance. Conventionally managed apricot orchard soil had the highest MI value of 1.48. The PPI value was highest in organically managed apricot orchards. All orchard soils were located within Quadrat B of the faunal analysis, indicating enrichment and structure. Regarding the diversity, richness and evenness of the distribution, conventional apricot soil had the highest species richness, while organic apple soil had the most even family distribution. Different management practices did not show marked differences in community composition and structure. The species richness of Fynbos soils was comparable to those of deciduous fruit orchards. Soil samples from eight different soil surface treatments were collected from an apple orchard in the Grabouw area. Treatments were combined according to the soil surface treatments received (chemical control of cover crops and weeds, mulch and mulch + effective micro-organism spray). Bacterivores were dominant in all soil treatments, with the least number being present in the chemical control (of cover crops and weeds) treatment. Sites which received chemical control of cover crops and weeds had higher levels of fungivores, compared to the levels at the other sites. High numbers of Rhabditidae occurred within mulch and mulch + effective micro-organism (EM) treatment sites, while high numbers of Aphelenchidae occurred in chemical control sites. The carnivorous family Ironidae only occurred in mulch + EM sites. Strong associations were found between soil surface applications and nematode families present within the soil. Chemical control (of cover crops and weeds) applications had the highest MI value, while values were equal for the other soil applications. The faunal analysis indicated that the mulch and the chemical control fell within Quadrat A, indicating enriched, but unstructured, soil, while the mulch + EM treatment fell within Quadrat B, indicating enrichment and structure, as well as good overall soil conditions. All the systems were dominated by bacterial decomposition pathways. Controversially, sites that received chemical control of the cover crops and weeds had the highest species richness of all three applications, as well as the highest level of diversity, according to the Simpson Index. As only the cover crops and the weeds were chemically controlled, the soil can be regarded as undisturbed, which explains the results obtained in this study. Clear differences in nematode community structure and composition were observed between the different soil applications in the apple orchard.

AFRIKAANSE OPSOMMING: Grond is 'n fundamentele, nie-hernubare hulpbron binne enige ekosisteem. Ten einde voedselproduksie vir die toenemende globale menslike bevolking te handhaaf, is dit noodsaaklik om maniere te ontwikkel om gesonde biologiese produktiwiteit en volhoubaarheid van landbougrond in stand te hou. Nematodes is een van die volopste Metazoa in alle gronde en vorm 'n integrale deel van die grond voedsel-web op verskeie trofiese vlakke. Hulle reageer vinnig op veranderinge binne hul omgewings, kan maklik ekstraheer en identifiseer word; en ook maklik in funksionele gildes ingedeel word. Nematodes het ook die potensiaal om insig oor te dra ten opsigte van die toestand van die grond voedsel-web. Hierdie studie het ten doel om vas te stel of nematodes geskikte bio-indikatore van grond gesondheid kan wees spesifiek vir die sagtevrugte bedryf in die Wes-Kaap. Drie verskillende doelwitte is gestel om die praktiese gebruik van nematode populasie samestelling as 'n instrument vir die meting van grond gesondheid te gebruik. Die doelwitte sluit in die nematode populasie samestelling, biodiversiteit en funksionaliteit binne natuurlike Fynbos; organies verboude versus konvensionele boorde; en die verskil in nematode populasie samestelling tussen verskillend behandelde en bestuurde grondpersele binne ʼn appel boord. Die nematode biodiversiteit en funksionaliteit vir elke perseel was bepaal deur die evaluering van die nematode voedselweb vir trofiese groep verspreiding en enumerering deur die Maturity Index (MI) en die Enrichment Index (EI), Strukturele Indeks (SI), Basale Indeks (BI) en Channel Index (CI) wat gebaseer is op die geweegde oorvloed van koloniseerder-persister gildes. Die funksionele gilde vir Fynbos monsters het aangedui dat die verryking en struktuur van enige gegewe perseel nie gebonde is aan ʼn bepaalde gebied nie, aangesien dit verteenwoordig was in elk van die vier kwadrante van die Fauna Analiseerder. Daar is gevind dat verskillende areas verskil in nematode diversiteit en funksionaliteit, wat hoofsaaklik geassosieer was met die dominante plant families en spesies in die omgewing. Die volopste nematode familie wat teenwoordig was in die Fynbos was Tylenchidae, wat plant-voedende nematodes is, en Cephalobidae, wat bakterie-voedend is. Tylenchidae en Cephalobidae het beide ʼn cp-waarde van twee, maar is verdeel in verskillende VIII tipes voedingsgroepe. Die cp-2 nematodes is verdraagsaam vir versteurings en kom in alle omgewings voor. Slegs een omnivoor familie is geïdentifiseer in Fynbos monsters, nl. die Dorylaimidae. Die gemiddelde MI waarde vir Fynbos was laag, met 'n gemiddelde waarde van 1.26. Hierdie waarde is ʼn aanduiding van die teenwoordigheid van taxa met verdraagsaamheid tot versteuring, wat op sy beurt 'n versteurde grond in die algemeen aangedui het. Die aantal plant-parasitiese nematodes binne die Fynbos-gronde was laag, wat ondersteun word deur die lae PPI-waarde van 0.85. Die waardes vir die diversiteit, spesie-rykheid en egaligheid was laag, wat dui op 'n lae nematode diversiteit, maar 'n egalige verspreidings onder families. Die Hill’s N0 indeks waarde was gelyk aan 'n gemiddelde van 8.0 en dui daarop dat in die algemeen agt nematode families teenwoordig sal wees in 'n Fynbos grondmonster. 'n Studie is gedoen om die biodiversiteit en funksionaliteit van nematodes wat verband hou met vrugteboorde wat organies en konvensioneel bestuur is te bepaal. Herbivore was dominant in alle boorde. Organiese appels het die laagste aantal herbivore en fungivore gehad en die hoogste aantal karnivore. Wanneer organiese en konvensionele appelkoosboorde met mekaar vergelyk is, was hoër getalle van plant-parasitiese nematodes gevind in die organiese boord. Criconematidae was teen ʼn groter aantal in die grond van die konvensionele appelkoosboord gevind. Met die vergelyking van organiese appelkose en appels word, is ʼn hoër aantal Criconematidae binne die organiese appelgrond aangetref. In die algemeen was hoër vlakke van plant-parasitiese nematodes gevind in die organiese appelkoosboord. Die MI het getoon dat alle boord waardes laer as 1.5 gehad het, wat daarop dui dat die gronde versteurd is. Die konvensioneel bestuurde appelkoosboord het die hoogste MI waarde gehad met ʼn vlak van 1.48. Die waarde vir die PPI was die hoogste in organies bestuurde appelkoosboorde. Alle boord gronde is geleë binne kwadrant B van die Fauna Analiseerder, wat dui op verryking met struktuur. Met betrekking tot die diversiteit, spesie-rykheid en egaligheid van die verspreiding van families, het konvensionele appelkoos grond die hoogste spesierykheid, terwyl die gronde van die organiese appelboord die mees egalige familie verspreiding vertoon het. Verskillende bestuurspraktyke nie toon nie merkbare verskille in die gemeenskap samestelling en struktuur nie. Die spesie-rykheid van Fynbos gronde is vergelykbaar met dié van sagtevrugte-boorde. Monsters is geneem van agt verskillende grondeoppervlak-behandelings in ‘n appelboord in die Grabouw area. Die behandelings is gekombineer volgens die grond toediening wat dit ontvang het (chemiese beheer van dekgewasse en onkruid, deklaag en ‘n deklaag + effektiewe mikro- IX organismes). Bakterievoedende nematodes was dominant in elke grondoppervlak-behandeling, met die minste teenwoordig in die behandelings wat chemiese beheer van die dekgewasse en onkruid ontvang het. Behandelings wat chemiese beheer van die dekgewasse en onkruid ontvang het, het ook hoër vlakke van fungivore in vergelyking met die ander behandelings. ʼn Hoë aantal Rhabditidae het voorgekom in grondmonsters van die deklaag en die deklaag + EM (effektiewe mikro-organismes) behandeling persele, terwyl ʼn groot aantal Aphelenchidae voorgekom het in chemiese beheer persele. Die predatoriese familie, Ironidae, het slegs voorgekom in persele wat die deklaag + EM behandeling ontvang het. Sterk assosiasies bestaan tussen grond behandeling en nematode families wat in die grond teenwoordig was. Die chemiese beheer behandeling het die hoogste MI waarde getoon, terwyl waardes vir die ander behandelings laer en gelyk was. Die fauna analise het daarop gedui dat die deklaag en chemiese beheer binne kwadrant A is en dus verryk, maar ook ongestruktureerd is. Die deklaag + EM behandeling het binne kwadrant B geval wat aandui op toestande van verryking en struktuur wat 'n goeie algehele grondtoestand tot gevolg gehad het. Al die stelsels is oorbruggingsweë wat oorheers was deur bakteriële ontbinding. Kontroversieel, het persele wat chemiese beheer van die dekgewasse en onkruid ontvang het, die hoogste spesierykheid van al drie behandelings getoon asook die hoogste vlak van diversiteit volgens die Simpson-indeks. Slegs die dekgewasse en onkruid is chemies behandel, nie die grond nie, en dus kan die grond as onversteurd beskou word en die resultate wat verkry is in die studie verklaar. Duidelike verskille in die nematode gemeenskap struktuur en samestelling is waargeneem tussen die verskillende grond behandelings in appel boorde.

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