Understanding the biodiversity impacts of invasive species : investigating changes in below- and above-ground mutualistic networks in response to invasions

Thesis (PhD)--Stellenbosch University, 2019.

ENGLISH ABSTRACT: Invasive non-native plant species threaten global biodiversity, and significantly impact on economic, agricultural, and ecosystem services. Specifically, invasive plants impact on native communities by altering ecological interactions between native species and by altering soil conditions, eventually impacting on whole ecosystems. For example, invasive nitrogen (N) fixing species such as legumes (Fabaceae) are some of best-known examples to cause such ecosystem-level impacts by elevating soil N content and altering soil bacterial community diversity and functionality. Considering that soil bacteria are essential for the health and diversity of plant communities, and ultimately to the functioning of ecosystems, such native system impacts ultimately lead invasive species in becoming ecosystem engineers, to the detriment of recipient environments. Considered a global biodiversity hotspot, South Africa’s Core Cape Subregion (CCR) is an area of international significance and is home to exceptional plant diversity. The generally strong link between above- and belowground community diversity implies that soil microbial diversity might mirror plant diversity in the CCR, e.g. like its unique fynbos vegetation. Despite this, virtually nothing is known about communities of CCR soils. Moreover, several invasive plants, notably Australian acacias, have severe impacts on CCR ecosystems. Thus, the aim of this thesis was to study the diversity and structure of CCR (fynbos) soil bacterial communities, and to investigate the impacts that invasive acacias have on them, together with impacts on soil nutrients, that ultimately lead to alteration in soil functioning. Furthermore, it is believed that the mutualistic associations that acacias form with nitrogen-fixing bacteria, known as rhizobia, might give them a competitive advantage when establishing, colonizing, and invading new environments. Thus, I also aimed to investigate whether differences in invasiveness between various acacias in South Africa can be explained by differences in the effectiveness of mutualistic rhizobial associations. To address the aims outline above, I made use of next-generation DNA sequencing (NGS) techniques and a paired design consisting of various sites with heavily acacia-invaded areas (as treatments) in close proximity to pristine, uninvaded fynbos areas. This allowed me to generate baseline data of the diversity and community composition of pristine fynbos soil bacterial communities, and how these relate to spatial and environmental attributes across different seasons. I then determined how invasive acacias alter fynbos soil bacterial communities, specifically in terms of community composition and diversity, and how impacts relate to the main spatial and environmental patterns of soil bacterial community turnover. Thereafter I investigated the impacts of acacias on soil chemistry and function (carbon, nitrogen, and phosphorus cycling), and determined what the links are between soil function, soil nutrient loads, and bacterial community composition, and whether acacia-induced changes translate into altered soil functionality. Finally, I shifted focus to differences between various acacia species in terms of their mutualistic rhizobial partnerships under field conditions, and asked whether there are differences in the rhizobial mutualistic associations and their effectiveness between widespread and invasive acacias, and localised non-invasive acacias. I found fynbos soils to be characterised by high bacterial diversities and unique bacterial assemblages characterised by specific dominant taxa. Turnover in pristine fynbos soil bacterial communities was mainly due to replacement, with little nestedness. Furthermore, turnover itself was largely driven by differences in abiotic soil conditions, specifically pH and NH4 + , as well as spatial separation. Together with these soil abiotic and spatial drivers, I found seasonality to play a significant role in shaping fynbos soil bacterial communities. Upon introducing the invasion component, I found acacias to significantly alter soil bacterial community composition, but not diversity, and that the presence of invasive acacias reduced the spatial variability across soil communities, such that community turnover could no longer be predicted by geographical distance, as was the case for pristine soils. This compositional change in bacterial communities was primarily driven by acacia-induced changes of soil pH and NH4 + . Furthermore, I found acacias to significantly increase levels of soil nitrogenous compounds (NO3 - , NH4 + , and total N), C and pH, and although such impacts were not consistent across all invaded sites, the direction of impacts were. Acacias significantly impacted on key aspects of soil functioning, as demonstrated by elevated activities of enzymes involved in nitrogen (urease) and phosphorous (phosphatase) cycling, but such impacts were site-specific. Changes in soil nitrogen and phosphorous content were correlated with changes in the activities of enzymes linked to their cycling, i.e. urease and phosphatase, respectively. For one of these enzymes (phosphatase), changes in soil bacterial community composition was correlated with enzymatic activity, suggesting that altered soil functionality is a direct result of acacia induced changes in soil nutrients, and an indirect result of alteration in bacterial community composition. Finally, I did not find any differences in richness, diversity and rhizobium community composition between localised and widespread invasive acacias in fynbos, and also did not find consistent differences in their ability to fix atmospheric nitrogen, except for some species by site comparisons, indicating differential symbiotic effectiveness between these species at specific localities. Thus, differential invasiveness of acacias in South Africa is likely linked to attributes other than mutualistic bacterial interactions, such as differences in propagule pressure, introduction pathways (e.g. forestry vs. ornamental) and intensity of plantings in the country.

AFRIKAANSE OPSOMMING: Uitheemse indringer plant spesies bedreig wêreldwye biodiversiteit, en het merkwaardige impakte op ekonomiese, landboukundige, en ekosisteem dienste. Indringer plante het spesifiek 'n impak op inheemse gemeenskappe deurdat hulle ekologiese interaksies tussen inheemse spesies verander, sowel as grondkondisies, wat op die uiteinde lei na 'n impak op ekosisteme as a geheel. Byvoorbeeld, indringer spesies wat atmosferiese stikstof (N) kan fikseer, soos peulplante (Fabaceae), is van die beste voorbeelde van spesies wat sulke ekosisteem-vlak impakte tot gevolg het en kan merkwaardige verskille veroorsaak in die ekosisteme waar hulle indring, soos byvoorbeeld om grond N vlakke te verhoog, asook om grond bateriële gemeenskaps diversiteit en funksie te verander. Sienende dat bakterieë noodsaaklik is vir die gesondheid en diversiteit van plant gemeenskappe, en uiteindelik die funksionering van ekosisteme as a geheel, lei sulke impakte van indringer akasias op inheemse sisteme daartoe dat hulle uiteindelik ekosisteem ingenieurs word, tot die nadeel van sulke inheemse sisteme. Suid Afrika se Kaapse Kern Subarea (KKS) word erken as biodiversiteits warmpunt (‘hotspot’) van internasionale belang en is die tuiste vir buitengewone plant biodiversitiet. Die sterk verband tussen bo- en ondergrondse gemeenskaps diversiteit impliseer dat grondmikrobiese diversiteit die plant diversiteit in die KKS kan weerspieël, soos in die unieke fynbosplantegroei. Ten spyte daarvan is feitlik niks bekend oor ondergrondse gemeenskappe van die KKS nie. Daarbenewens het verskeie indringerplante, veral Australiese akasias, 'n ernstige impak op KKS ekostelsels. Die doel van hierdie proefskrif was dus om die diversiteit en struktuur van KKS (fynbos) grondbakteriese gemeenskappe te bestudeer en die impakte wat indringer akasias op hulle het, te ondersoek, tesame met die impakte op grond nutriente wat uiteindelik tot verandering in grondfunksionering kan lei. Verder word daar geglo dat die mutualistiese assosiasies wat akasias met stikstofbindende bakterieë genaamd rhizobia vorm, hulle 'n mededingende voordeel gee wanneer hulle in nuwe omgewings vestig en indringer populasies vorm. Ek het daarop gemik om te ondersoek of verskille in indringer potensiaal tussen verskillende akasias in Suid-Afrika verklaar kan word deur verskille in die effektiwiteit van rhizobiale assosiasies.Om die bogenoemde doelstellings aan te spreek, het ek gebruik gemaak van volgende generasie DNA- basis volgorde bepalings (NGS) tegnieke en 'n gepaarde ontwerp wat bestaan uit verskillende terreine waar akasias in hoë digthede voorkom (as behandelings) in die nabyheid van ongerepte fynbosgebiede. Dit het my toegelaat om verwysingsdata te genereer van die diversiteit en samestelling van die ongerepte fynbos grondbakteriese gemeenskappe, en hoe dit verband hou met ruimtelike en omgewingskenmerke oor verskillende seisoene. Ek het toe vasgestel hoe indringer akasias fynbos grondbakteriese gemeenskappe verander, spesifiek in terme van gemeenskap samestelling en diversiteit, en hoe dié impakte verband hou met die belangrikste ruimtelike en omgewingspatrone van grondbakteriese gemeenskapsomset. Daarna het ek die impakte van akasias op grond chemie en funksie (koolstof, stikstof, en fosfor siklusse) bestudeer, met die doel om te bepaal of grond funksie gekoppel is aan grond nutrient inhoud en bateriële gemeenskap samestelling, en of sulke veranderinge wat veroorsaak is deur akasias kan lei na veranderinge in grond funksie. Laastens het ek my fokus geskuif na die verskille tussen verskeie akasia spesies in terme van hul mutualistiese assosiasies met rhizobia onder natuurlike omstandighede en gevra of daar verskille bestaan tussen die rhizobiale assosiasies, en hul doeltreffendheid, tussen wydverspreide indringer akasias en gelokaliseerde en wydverspreide akasias. Ek het ek gevind dat fynbos grond gekenmerk word deur hoë bateriële diversiteit en dat sulke gronde unieke bateriële samestellings het wat gekenmerk word deur spesifieke dominante taxa, en dat omset in grondbakteriese gemeenskappe grootliks as gevolg van vervanging was, met lae nestedness. Verder was omset self hoofsaaklik gedryf deur verskille in abiotiese grond kondisies, spesifiek pH en NH4 +, tesame met ruimtelike verdeling. Tesame met hierdie grond abiotiese en ruimetlike drywers, het ek gevind dat seisoene 'n merkwaardige rol speel in die vorming van fynbos grond bateriële gemeenskappe. Ek het gevind dat indringer akasias die samestelling van grond bateriële gemeenskappe merkwaardig verander, maar nie die diversiteit nie, en dat hulle die geografiese variasie van grond gemeenskappe verminder, sodanig dat gemeenskap omset nie meer voorspel kon word die geografiese afstand nie, soos wat die geval was vir ongerepte fynbos gronde. Die verandering in samestelling van grond grondbakteriese gemeenskappe as gevolg van akasias was hoofsaaklik gedryf deur veranderinge in grond pH en NH4 + . Verder het ek gevind dat akasias 'n merkwaardige verhoging in grond stikstofagtige verbindings (NO3 - , NH4 + , en totale N), C en pH veroorsaak het, en alhoewel die impakte nie ooreenstemmend was oor al die ingedringde areas nie, was die rigting van sulke impakte wel. Akasias het 'n merkwaardige impak gehad op sleutel aspekte van grond funksie, soos bewys deur verhoogde vlakke van aktiwiteite van ensieme wat betrokke is by stikstof (urease) en fosfor (fosfatase) sirkulering, maar sulke impakte was area-spesifiek. Veranderinge in grond stiksof en fosfor inhoud was gekorreleer met veranderinge in ensiem aktiwiteite vir urease en fosfatase, onderskeidelik. Die verandering in grondbakteriese samestelling was vir een van hierdie ensieme (fosfatase) gekorreleer met ensiem aktiwiteit, wat daarop dui dat veranderinge in grond funksie 'n direkte resultaat is van veranderinge in grond nutriente as gevolg van akasias, en 'n indirekte resultaat van die verandering in grondbakteriese gemeenskap samestelling. Laastens het ek geen verskille gevind in die rykheid, diversiteit, en rhizobium gemeenskap samestelling tussen gelokaliseerde en wydverspreide indringer akasias in fynbos nie. Ek het ook nie ooreenstemmende verskille gevind in hulle vermoëns om atmosferiese stikstof te bind nie, behalwe vir sekere spesie by area vergelykings, wat daarop dui dat symbiotiese effektiwiteit tussen die spesies by spesifieke lokaliteite verskil. Dus, die verskille in indringingsvlakke van akasias in Suid-Afrika is moonltlik gekoppel aan eienskappe anders as mutualistiese bateriële interaksies, soos byvoorbeeld verskille is propaguledruk, redes vir vrystelling (bv. bosbou teenoor tuinbou) en die intensiteit van aanplantings in die land.

Doctoral