Agroecosystem diversification for sustainability : the effects of crop rotation on soil microbial diversity, fertility and yield

Venter, Zander Samuel (2016-03)

Thesis (MScAgric)--Stellenbosch University, 2016.

Thesis

ENGLISH ABSTRACT: Agricultural intensification can involve the simplification of agroecosystems to crop monocultures requiring agrochemicals to maintain soil fertility and control pests. This can have negative impacts on the ecosystem services flowing to and from agroecosystems and thus, more sustainable management practices are necessary. Broader ecological theories propose that ecosystem biodiversity is important for ecosystem function. Within agriculture, increasing aboveground diversity through crop rotation, a component of conservation agriculture, can enhance the ecosystem services supporting an increase in cash-crop yield. The extent to which the belowground microbial diversity can be manipulated through crop rotations and may facilitate the yield increase is unclear. This thesis aimed at investigating (1) the relationship between above and belowground diversity in crop rotation systems, and (2) the relationship between diversity in (1) and agroecosystem function in terms of soil fertility, including nitrogen fertility, and crop yield. A quantitative review of the literature using a meta-analysis of 27 studies from around the world found that soils under a higher diversity of crops in rotation produced higher microbial richness (+15.11%) and diversity (+3.36%) scores. This effect was significantly influenced by the type of microbial analysis method used, the length of the study trial, and the percentage annual ground cover. There was a high between-study heterogeneity and no correlation to soil nitrogen fertility. A field study at Langgewens Experimental Farm (Western Cape Department of Agriculture’s 19-year wheat-legume crop rotation trial in the Swartland Local Municipality of South Africa) added to the meta-analysis. Community level physiological profiling (CLPP) and automated rRNA intergenic spacer analysis (ARISA) were used as measures of functional and genetic microbial diversity, respectively. Increasing crop diversity through rotations of wheat with medic (Wm) or a combination of medic and clover (Wmc) resulted in greater wheat plant stem length and N concentrations when compared to wheat monoculture (WW). This effect seemed to be less linked with microbial diversity per se than with the Rhizobium species present because both microbial analyses found no differences in soil microbial activity, richness or diversity with increasing crop diversity. The lack of relationship between above and belowground diversity is likely due to other abiotic drivers of microbial community structure such as P availability, Na and K excess, and pH, all of which correlated to microbial activity and functional richness in our study. The role that microbial diversity plays in the agroecosystem diversity-function relationship remains complex as revealed by the lack of correlation between functional and genetic diversity scores. However, the relation between crop diversity and functional components including wheat yield and soil N followed a hump-shaped curve. The results of this thesis suggest that soil biodiversity and function are decoupled in agroecosystems. This provides support for the hypothesis that ecosystem function may be a product of either specific productive species (selection effect), or the facilitative interaction of multiple species (complementarity effect). Further investigation into the role of specific functional microbial groups in the yield increase of crop rotation systems using next-generation sequencing is required.

AFRIKAANSE OPSOMMING: Die verhoging van landbou intensiteit behels die omskakeling van landbou ekosisteme na monokultuur, wat landbou-chemikalieë vereis om grondvrugbaarbeid te handhaag en peste in toom te hou. Hierdie praktyke het 'n negatiewe impak op ekosisteemdienste wat vloei van of na die landbou-ekosisteme. Dit vereis meer volhoubare landboubestuurspraktyke. Wyer ekologiese teorieë stel voor dat ekosisteem biodiversiteit 'n belangrike rol speel in die funksie van die ekosisteem. Binne landboupraktyke, kan 'n toename in bogrondse diversiteit deur wisselbou, die ekosisteemdienste verbeter, wat lei tot 'n toename in die opbrengs in kontant gewasse. Die mate waartoe die ondergrondse mikrobiese diversiteit gemanipuleer kan word, is nog onduidelik. Hierdie tesis beoog om (1) die verwantskap tussen die bogrondse en ondergrondse diversiteit in wisselbousisteme, en (2) die verwantskap tussen die diversiteit in (1) en die lanbouekosisteem funksie te ondersoek in terme van grondvrugbaarheid, insluitend stikstofvrugbaarheid, en gewasopbrengs. ‘n Kwantitatiewe oorsig van literatuur deur gebruik te maak van ‘n meta-analise van 27 studies van regoor die wêreld, het gevind dat grond met 'n hoër diversiteit van gewasse in wisselbou gelei het tot ‘n hoër mikrobiese (+15.11%) tellings, terwyl die effek van diversiteit (+3.36%) nie beduidend was nie. Die effek van diversiteit was beduidend beïnvloed deur die tipe mikrobiese-analitiese metode wat gebruik was, die lengte van die toetsperiode en die persentasie van jaarlikse grondbedekking. Die heterogeniteit tussen studies was hoog en daar was geen korrelasie met grond stikstofvrugbaarheid nie. ‘n Veldstudie by Langgewens proefplaas (Weskaap Departement van Landbou se 19-jaar koring-peulplant wisselbou toets in die Swartland plaaslike munisipaliteit,Suid-Afrika) is bygevoeg tot die meta-analiese. Gemeenskapvlak fisiologiese profiel bepalin (GVFP) en automatiese rRNS intergeniese spasie analiese (ARISA) is onderskeidelik gebruik as maatstawwe van funksionele en genetiese mikrobiese diversiteit. Toenemende gewas diversiteit deur wisselbou van koring met medic (WM) of ‘n kombinasie van medic en klawer (Wmc) het ‘n groter koringplant stamlengte en N konsentrasie tot gevolg gehad wanneer dit vergelyk word met koring monokultuur (WW). Die effek blyk minder gekoppel te wees met mikrobiese diversiteit per se as met die Rhizobium spesies wat betrokke is. Mikrobiese analieses van beide sisteme het gevind dat daar geen veranderinge in die grond se mikrobiese aktiwiteit, rykdom of diversiteit is, met toename in gewasdiversiteit nie. Die afwesigheid van ‘n verhouding tussen die bogrondse en ondergrondse diversiteit is waarskynlik ook as gevolg van ander abiotiese drywers van die mikrobiese gemeenskapstruktuur soos beskikbaarheid, oormaat in Na en K, en pH, wat alles gekoppel is aan mikrobiese-aktiwiteit en funksionele rykdom in die studie. Die rol wat mikrobiese diversiteit speel in die agro-ekosisteem diversiteit funksie bly kombleks soos uitgewys deur die gebrek aan verwantskap tussen die funksionele en genetiese diversiteitstellings. Nietemin, die verhouding tussen gewas-diversiteit en funktionele komponente, insluitend koringopbrengs en grond N, het ‘n bultvormige kurwe gevolg. Die resultate van hierdie tesis dui daarop dat biodiversiteit en funksie ontkoppel is in landbou-ekosisteme. Dit ondersteun die hipotese dat ekosisteem-funksie ‘n produk kan wees van of spesifieke produktiewe spesies (seleksie effek), of die fasiliterende interaksie van verskeie spesies (komplimentêre effek). ‘n Verdere ondersoek in die rol van spesifiek funksionele groepe in die opbrengs toename van wisselbou sisteme word benodig deur gebruik te maak van volgende-generasie DNA volgorde bepaling.

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