published_or_final_version / Botany / Master / Master of Science

<p>The microbial life of sub-Antarctic islands plays a key role in the islands ecosystem, with microbial activities providing the majority of nutrients available for primary production. Knowledge of microbial diversity is still in its infancy and this is particularly true regarding the diversity of micro-organisms in the Antarctic and sub-Antarctic regions. One particularly important functional group of micro-organisms is the diazotrophs, or nitrogen-fixing bacteria and archaea. This group have not been well studied in the sub-Antarctic region, but play an important role in the nutrient cycling of the island. This thesis explored the diversity of nitrogen-fixing organisms in the soil of different ecological habitats on the sub-Antarctic Marion Island.</p>

<p>Soil communities are regarded as among the most complex and diverse assemblages of microorganisms with estimated bacterial numbers in the order of 10â?¹ cells.gâ?»&sup1 / . Studies on extreme soils however, have reported lower cell densities, supporting the perception that the so-called extreme environments exhibit low species diversity. To assess the extent of microbial diversity within an extreme environment, the mineral soils of the Dry Valleys, Ross Dependency, Eastern Antarctica were investigated using 16S rDNA analysis.</p>

Wheat crops are known to be devastated by infections of soil-borne pathogens, especially the fungus <i>Gaeumannomyces graminis </i>var. <i>tritici</i> (Ggt) that causes ‘take-all’. Plant growth promoting rhizobacteria (PGPR) such as <i>Pseudomonas fluorescens</i> have received much attention as biocontrol agents against Ggt, mainly due to their ability to produce antibiotics. The polycetide secondary antimicrobial metabolite 2,4-diacetylphloroglucinol (DAPG) is produced by a number of fluorescent pseudomonad strains and is known to suppress Ggt. Another soil microbial group which have been under investigation for their biocontrol potential against Ggt, are arbuscular mycorrhizal (AM) fungi which have the potential to out-compete Ggt and improve host plant nutrition and vigour. In this thesis, I report results from experiments that investigate interactions among AM fungi, Ggt, and DAPG-producing bacteria. A central hypothesis is that carbon flow from plants and AM fungi stimulates DAPG production. I therefore focus on interactions among AM fungi, Ggt and bacteria <i>in vivo</i> with wheat plants and <i>in vitro</i> with only fungal exudates. The synergistic co-operation of pseudomonads and AM fungi against Ggt was demonstrated and the fungal exudates (from AM and Ggt) produced both <i>in vitro</i> and <i>in vivo</i> increased DAPG production by <i>P. fluorescens</i>. The ecology and functioning of beneficial AM fungi was found not to be influenced by the presence of either Ggt or DAPG, highlighting the potential sustainable suppression of “take all” in wheat rhizosphere.

Master of Science / Department of Agronomy / Ganga M. Hettiarachchi / Human activities have the potential to alter soil biochemical properties in a number of different ways. This thesis will focus on how agricultural practices (tillage and cropping system), climate change, and urban soil pollution (primarily lead and arsenic) affect soil biochemical properties. Two incubation studies were conducted to determine how human activities influence soil biochemical properties. The first study focused on how altered temperature and moisture regimes affected soil properties from four different agroecosystems. Four different soils were incubated under two different soil preparation methods (sieved <4mm and <0.25 mm), three different temperature treatments (12, 24, and 36°C), and two different moisture treatments (field capacity and 80% of field capacity) for 180 days. Destructive samples were taken at 7, 30, 60, 120, and 180 days and the soil microbial community was analyzed using phospholipid fatty acid analysis (PLFA). The second study investigated how soil amendment treatments (Mushroom Compost and Composted Biosolids) of an industrially contaminated site affected the biochemical properties of that soil. Surface soil samples collected 435 days after compost addition from urban garden test plots located adjacent to a former rail yard in Monon, Indiana. Soils were incubated for 30 days to stimulate microbial activity. Following incubation, the soil was analyzed for PLFA, soil enzymes, and available metal fractions. In the first study the greatest differences were found between the <4mm and the <0.25 mm size fractions – which highlights the effect of soil aggregation and structure on microbial populations. After aggregation effects, temperature treatment had the next largest effect on microbial populations, with the greatest biomass in the middle (24°C) treatment. The second study assessed different soil amendments on soil microbial properties and metal availability. Composted biosolids reduced metal availability and increased microbial enzyme activity and biomass.

Burkholderia cepacia complex (Bcc) bacteria reside in soil, plant rhizospheres, and water, but the prevalence of Bcc in outdoor environments is not clear. In this study, we sampled a variety of soil and rhizosphere environments with which people may have contact: playgrounds, athletic fields, parks, hiking trails, residential yards and gardens. A total of 9l soil samples was obtained from three large U.S. cities (Philadelphia, PA, Cleveland, OH, and Portland, OR). In the first phase of the study, putative Bcc isolates were recovered on Burkholderia cepacia selective agar (BCSA) and trypan blue tetracycline medium (TBT). Isolates were sent to the Burkholderia cepacia Referral Laboratory and Repository, where they were identified using biochemical tests, growth at 32��C, and polymerase chain reaction (PCR) assays targeting both rRNA and recA gene sequences. Bcc isolates were genotyped by using RAPD, PFGE and rep-PCR. A total of 1013 bacterial isolates were examined, and 68 were identified as B. cepacia complex. The majority of these were B. pyrrocinia or genomovar VII (B. ambifaria); however, a few genomovar III isolates were also recovered. Fourteen (15%) of 91 soil samples yielded Bcc isolates. In the second phase of the study, DNA was extracted from 87 of the 91 soil samples and examined with PCR assays targeting Bcc 16S rRNA gene sequences. By using assays developed by LiPuma et al. (1999), 82% of the soil samples were positive for at least one Bcc genomovar, whereas 94% of samples were positive for at least one Bce genomovar using the Bauernfeind et al. (1999) assay system. Selected amplicons generated from four soil samples were cloned, and plasmids from multiple transformants (total=120) were screened by RFLP analysis. Among the clones evaluated from three of four soil samples, 90% or more had the "Burkholderia" RFLP pattern. In the remaining soil sample, only 9.5% of the evaluated clones displayed this profile. Sequence analysis of the 463bp 16S rRNA inserts from eight clones with the "Burkholderia" RFLP pattern indicated that all were from members of the Bcc. However, the four soil samples from which these clones were generated did not yield isolates identified as Bcc. This study indicates that the use of selective media may not be the best way to estimate the environmental prevalence of Bcc in soils. The natural populations of Bcc in soils with which people commonly have contact may be much higher than previously estimated. / Graduation date: 2002

Graduation date: 2000

Graduation date: 1997

Graduation date: 1992

Graduation date: 1992