The effect of fire scars on microbial diversity of fynbos soil

Smart, Ricardo Virgill (2017-12)

Thesis (MSc)--Stellenbosch University, 2017.

Thesis

ENGLISH ABSTRACT: Microbial communities (bacteria, archaea, fungi, protista and viruses) are essential for the maintenance of a healthy balance in soil ecosystems. There are many factors that influence and disrupt this balance, including invasive species and fire events which disturb the properties and microhabitats of soil. Riparian zones are not typically exposed to fire. However, when the riparian zones are exposed to fire, it may have significant consequences for the natural patterns and processes of a soil ecosystem and the soil microbial communities. Invasive alien woody species such as Acacia and Eucalyptus spp. have become ubiquitous across riparian environments, affecting water and nutrient cycling and reducing plant diversity. However, the approaches to clear invasive species may also have negative consequences for ecosystem functioning. The ‘slash and burn’ technique is a biomass management tool that uses the felling of invasive stands, which are then stacked to build a pile (from dead plant biomass) and burnt. This study determined the effect of burning (the ‘slash and burn’ technique) of invasive biomass (Acacia and Eucalyptus spp.) on soil bacterial and fungal diversity and community structure in fynbos riparian zones (Western Cape, South Africa). The sites chosen for this study were within fynbos regions invaded by Acacia mearnsii (also known as black wattle) or Eucalyptus camaldulensis (river red gum). Four study sites were chosen, each at different statuses of invasion. These sites were Bainskloof, Rawsonville, Robertson and Wellington. Before the mechanical removal of invasive species, the Bainskloof and Rawsonville sites consisted predominantly of A. mearnsii, with a small percentage cover of Eucalyptus spp. at the Rawsonville site. The Robertson and Wellington sites consisted predominantly of E. camaldulensis, with a small percentage cover of Acacia spp. at the Wellington site. Changes in the microbial diversity and community structure were assessed using automated ribosomal intergenic spacer analysis (ARISA) fingerprinting. Microbial diversity profiles of ARISA were determined by means of the Shannon (H’) and Simpson’s complement (1-D) indices. Microbial community structure profile of ARISA was evaluated by means of Analysis of Similarity (ANOSIM), cluster analysis and non-metrical multidimensional scaling (NMDS). The Pearson correlation coefficient (PCC) analysis was used for the correlation between the chemical properties and microbial diversity (H’). Whereas, the principle component analysis (PCA) was used to determine which chemical properties may explain the variation of microbial community structure post-fire. This study showed that the ‘slash and burn’ of Eucalyptus biomass had a greater impact on the soil microbial communities compared to the ‘slash and burn’ of Acacia biomass. The data indicated that the ‘slash and burn’ of Acacia biomass (Bainskloof) did not affect the bacterial diversity (H’) post-fire. In contrast, the ‘slash and burn’ of Eucalyptus biomass (Robertson and Wellington; also Rawsonville, where some Eucalyptus biomass was present in the piles) led to a steep decrease in bacterial diversity (H’) immediately post-fire which remained relatively low a year after the burn event. Furthermore, the ‘slash and burn’ of Acacia and Eucalyptus biomass had no effect on the fungal diversity (H’). This, in turn, resulted in no variation of fungal diversity (H’) within and between invasion sites throughout the study. Post-fire, all sites demonstrated a shift in microbial community structure. In addition, all the sites showed three distinct bacterial community structures separated by different sample times. The unique microbial community structure in the Bainskloof site, a year after the burn event, could be due to the disturbance of a flood. The unique bacterial community structures in the Eucalyptus (Robertson and Wellington) and Rawsonville sites, a year after the burn event, are likely due to the successional changes of the bacterial communities after the ‘slash and burn’. Furthermore, the fungal community structures post-fire and a year after the burn event in the Eucalyptus sites could not be delineated as separate clusters. This was in contrast to the results in the Rawsonville site where the post-fire fungal community structure was different from the community structure a year after the burn event. Moreover, the fungal community structures in the Eucalyptus and Rawsonville sites a year after the burn event were similar. This similarity could possibly be due to the post-fire dominant fungal species that are beneath the soil surface layer where fire occurred or from adjacent areas around the burnt piles. These post-fire dominant fungal species have the capacity to disperse into the burnt areas by means of mycelial expansion from deeper to surface soil profiles or from the margins of the burnt piles into the burnt areas. The sites exposed to the ‘slash and burn’ of Eucalyptus biomass showed that soil pH served as the strongest soil abiotic indicator for bacterial diversity (H’). This finding was not evident in the Bainskloof site, which was exposed to the ‘slash and burn’ of Acacia biomass. In this study, all the sites showed that the ‘slash and burn’ of Acacia and Eucalyptus biomass leads to an increase in soil pH. However, the bacterial diversity (H’) showed different trends between invasion sites post-fire. The ‘slash and burn’ of Eucalyptus biomass resulted in a decrease in bacterial diversity (H’). Whereas, the ‘slash and burn’ of Acacia biomass did not affect the bacterial diversity (H’) post-fire. As for the fungal communities, no soil abiotic properties served as a useful indicator for the fungal diversity (H’). The soil pH, EC and PO4 concentration explained the most variation of microbial communities in the sites exposed to the ‘slash and burn’ of Eucalyptus biomass. These trends were not observed after the ‘slash and burn’ of Acacia biomass at the Bainskloof site. At this site, no variation in EC and PO4 concentration was recorded immediately post-fire. However, EC and PO4 concentration a year after the burn event was relatively higher compared to the conditions pre-fire. As for the sites exposed to the ‘slash and burn’ of Eucalyptus biomass, the soil pH, EC and PO4 concentration showed a steep increase immediately post-fire which remained relatively high a year after the burn event. ‘Slash and burn’ of Eucalyptus biomass left a patch where the fynbos vegetation did not recover. It is possible that the ‘slash and burn’ of Eucalyptus biomass may have damaged the roots and mycorrhizal fungi in the soil that consequently decreased the rate and capacity of recolonization in burnt areas. For future research, it will be useful to investigate the effect of ‘slash and burn’ of invasive biomass on specific functional groups (i.e. mycorrhizal fungi, ammonifiers and N-fixers) in the riparian zones of fynbos. It will also be of value to evaluate the recovery of these functional groups (if possible) post-fire and to determine what it means for the restoration of fynbos vegetation. ‘Slash and burn’ of Acacia biomass, however, is unclear due to the interference of a flood that occurred at the Bainskloof site during the trial period. The flood disturbed the burnt areas and led to the re-establishment of A. mearnsii. Therefore, for future research, an observational study may be considered to assess whether fynbos vegetation will recover after ‘slash and burn’ of Acacia biomass. Taken together, the results demonstrated a shift in microbial communities post-fire. However, the microbial diversity (H’) remained the similar after the ‘slash and burn’ of Acacia biomass.

AFRIKAANSE OPSOMMING: Mikrobiese gemeenskappe (bakterieë, archaea, fungus, protista en virusse) is noodsaaklik vir hul funksie om ’n gesonde balans te behou in grond. Daar is baie faktore wat hierdie balans beïnvloed en ontwrig, insluitende uitheemse bome en brande wat die eienskappe en mikrohabitats van grond versteur. Rivieroewers ervaar gewoonlik nie ’n brand nie, maar indien wel kan dit moontlik ’n beduidende invloed hê op die natuurlike patrone en prosesse van die grond ekosisteem en die grondmikrobiese gemeenskappe. Uitheemse indringer bosagtige spesies soos Acacia en Eucalyptus spp. het alomteenwoordig geword in oeweromgewings, en het sodoende die water- en voedingstofsiklusse beïnvloed en het plantdiversiteit verminder. Pogings om die indringerspesies te verwyder het egter negatiewe gevolge vir die funksionering van die ekosisteem. Die ‘sny-en-brand’ tegniek word gebruik om die biomassa te beheer en bestaan uit die afkap van uitheemse bome, waarvandaar ’n ophoping van dooie plant biomassa gemaak word en daarna gebrand word. Hierdie studie fokus op die effek van vuur (die ‘sny-en-brand’ tegniek) van uitheemse bome (Acacia en Eucalyptus spp.) op die grondbakteriese en fungus diversiteit en gemeenskapstruktuur in riveroewers van fynbos (Wes-Kaap, Suid-Afrika). Die fynbos rivieroewers wat bestudeer word in hierdie studie is bedreig deur Acacia mearnsii (black wattle) of Eucalyptus camaldulensis (river red gum). Vier studie areas was gekies, waarvan twee van die studie areas bedreig was deur A. mearnsii en E. camaldulensis, onderskeidelik. Voor die verwydering van uitheemse bome, was die Bainskloof en Rawsonville areas gedomineer deur A. mearnsii, met ’n lae persentasie van Eucalyptus spp. by die Rawsonville area. Die Robertson en Wellington areas was gedomineer deur E. camaldulensis, met ’n lae persentasie van Acacia spp. by die Wellington area. Veranderinge in die mikrobiese diversiteit en gemeenskapstruktuur was bepaal deur die geoutomatiseerde ribosomale intergeniese spasie analise (ARISA) vingerafdruk metode. Hierdie metode is gebruik om die grondmikrobiese diversiteit en gemeenskapstruktuur te analiseer. Die mikrobiese diversiteitsprofiel van ARISA was bepaal met die gebruik van die Shannon (H’) indeks en Simpson komplement (1-D) indeks. Die mikrobiese gemeenskapstruktuur profiel van ARISA is geëvalueer met behulp van die Analise van Soortgelykheid (ANOSIM), kluster analise, en die nie-metriese multidimensionele skaling (NMDS). Die Pearson-korrelasiekoëffisiënt (PCC) analise is gebruik om die korrelasie tussen die chemiese komponente en die mikrobiese diversiteit te bepaal. Die beginselkomponent-analise (PCA) is gebruik om te bepaal watter chemiese eienskappe die variasie in mikrobiese gemeenskapstruktuur na die brand veroorsaak. Die studie bewys dat die ‘sny-en-brand’ van Eucalyptus biomassa ʼn groter impak het op die mikrobiese gemeenskappe, in vergelyking met die ‘sny-en-brand’ van Acacia biomassa. Die ‘sny-en-brand’ van Acacia biomassa (Bainskloof) het geen effek op die bakteriese diversiteit (H’ en 1-D) gehad nie. In teenstelling, het die ‘sny-en-brand’ van Eucalyptus biomassa (Robertson en Wellington; sowel as Rawsonville, wat ’n aantal Eucalyptus biomassa bevat het binne die ophopings), tot ʼn afname in bakteriese diversiteit (H’ en 1-D) gelei, wat gevolglik konstant gebly het tot ’n jaar na die brand. Met betrekking tot die fungus diversiteit (H’ en 1-D), het die ‘sny-en-brand’ van Acacia en Eucalyptus biomassa geen effek op die fungus diversiteit (H’ en 1-D) gehad nie. Die fungus diversiteit was soortgelyk tussen studie areas, voor en na die brand. Na die ‘sny-en-brand’ van Acacia en Eucalyptus biomassa, het al die studie areas ’n verskuiwing in grondmikrobiese gemeenskapstruktuur getoon. Die bakteriese gemeenskapstruktuur, in al die studie areas, was verskillend by elke monsternemingsessie. Die oorstroming in die Bainskloof area het gelei tot ’n unieke mikrobiese gemeenskapstruktuur, ’n jaar na die brand. Die unieke bakteriese gemeenskapstrukture in die Eucalyptus en Rawsonville areas, ’n jaar na die brand, is as gevolg van die opeenvolgende veranderinge van bakteriese gemeenskappe na die brand. Die fungus gemeenskapstruktuur na die brand, in die Eucalyptus areas, was soortgelyk aan die gemeenskapstruktuur ’n jaar na die brand. In teenstelling, die fungus gemeenskapstrukture in die Rawsonville area, na die brand en ’n jaar na die brand, was verskillend. Verder, die fungus gemeenskapstrukture in die Eucalyptus en Rawsonville areas, ’n jaar na die brand was soortgelyk. Hierdie ooreenkoms kan moontlik toegeskryf word aan die dominante fungus spesies na die brand, wat voorkom onder of aan die rante van die verbrande grondoppervlakte. Hierdie dominante fungus spesies het die vermoë om oor die verbrande grondoppervlakte te versprei deur middel van miselium uitbreiding van dieper na grondoppervlak, of van die rante na binne die verbrande grondoppervlakte. Die areas wat gebrand was met die Eucalyptus biomassa het getoon dat die grond pH as ’n sterk abiotiese indikator dien vir die grondbakteriese diversiteit (H’). Dit was nie die geval in die Bainskloof area wat deur die Acacia biomassa gebrand was nie. Al die studie areas het getoon dat die ‘sny-en-brand’ van Acacia en Eucalyptus biomassa die grond pH verhoog het, maar die neiging in bakteriese diversiteit (H’) na die brand was verskillend. Na die ‘sny-en-brand’ van Eucalyptus biomassa was daar ’n afname in bakteriese diversiteit (H’). In teenstelling, was die bakteriese diversiteit (H’) nie geaffekteer na die ‘sny-en-brand’ van Acacia biomassa nie. In hierdie studie, was daar geen korrelasie getoon tussen die abiotiese eienskappe en fungus diversiteit (H’) nie. Die grond pH, elektriese geleidingsvermoë (EC) en fosfaat (PO4) konsentrasie verduidelik die meeste variasie tussen die mikrobiese gemeenskapstrukture na die brand, in die areas wat gebrand was met die ‘sny-en-brand’ van Eucalyptus biomassa. Hierdie tendense was nie gevind na die ‘sny-en-brand’ van Acacia biomassa (Bainskloof) nie. Na die ‘sny-en-brand’ van Acacia biomassa was daar geen variasie in EC en PO4 konsentrasie getoon nie. In teenstelling, die areas wat gebrand was met die ‘sny-en-brand’ van Eucalyptus biomassa het getoon dat daar ’n toename is in grond pH, EC en PO4 konsentrasie na die brand, wat gevolglik konstant gebly het tot ’n jaar na die brand. Die ‘sny-en-brand’ van Eucalyptus biomassa het gelei tot brandletsels wat die plantegroei van fynbos spesies verhoed het. Dit is moontlik dat die ‘sny-en-brand’ van Eucalyptus biomassa die wortels en mikorrisa in die grond vernietig het wat gevolglik die herstel van plantegroei in gebrande areas beïnvloed het. Vir verdere navorsing sal dit nuttig wees om die effek van vuur (die ‘sny-en-brand’ tegniek) van uitheemse bome op spesifieke funksionele groepe (soos byvoorbeeld mikorrisa en N-fikseerders) in die oewersones van fynbos te bestudeer. Dit sal ook van waarde wees om die herstel van hierdie funksionele groepe (indien moontlik) na die brand te evalueer en te bepaal wat hierdie effek op die herstel van fynbosplantegroei mag hê. Die ‘sny-en-brand’ van Acacia biomassa is onbekend as gevolg van die oorspoeling in die Bainskloof area gedurende die proefperiode. Die vloed het die verbrande oppervlakte versteur en het gelei tot die herstel van A. mearnsii. Op grond hiervan, mag dit van waarde wees om te bepaal of die fynbos plantegroei sal herstel na die ‘sny-en-brand’ van Acacia biomassa. Neem kennis dat daar ʼn verskuiwing in mikrobiese gemeenskappe getoon was en dat die mikrobiese diversiteit (H’) konstant gebly het na die ‘sny-en-brand’ van Acacia biomassa.

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