Estuaries are valuable economic resources to humans. However, changes in these ecosystems, such as alteration in nutrient availability, can impose eutrophic pressures. Traditionally, estuaries have been monitored through chemical analyses that measure factors such as sediment oxygen demand (SOD) and reduced forms of Fe(II), Mn(II), and H2S. These methods are time consuming and have been proven to be unreliable. This study was conducted to determine if using T-RFLP analysis could be used as a proxy for some of the current methods used to monitor eutrophication. Using SPSS to perform a principle component analysis, it was determined that connections can be made between the genetic fingerprints of microbial communities in estuaries and the biogeochemical markers that are currently used to monitor eutrophication. This method can potentially replace the current methods by allowing scientists to measure more sites rapidly and with reproducibility.

This study examined the effect of in-situ biosparging on pentachlorophenol (PCP) degradation and bacterial communities in PCP contaminated groundwater. Bacteria were identified by sequencing the 16s rDNA fragment from DNA extracted from groundwater cultures and comparing those sequences to a database using a basic local alignment search tool, BLAST. The PCP-degraders Burkholderia cepacia and Flavobacterium (Sphingobium) chlorophenolicum were identified in multiple wells, as were the 4-chlorophenol degrader Herbaspirillum sp., and the common soil bacteria Pseudomonas sp., Aquaspirillum sp., and Rhodocista sp., among others. Numerous bacterial samples also appeared in the results as “uncultured”. Bacterial community changes were observed using terminal restriction fragment length polymorphism (TRFLP) analysis to identify operational taxonomic units of bacteria at various locations inside and outside the biosparging zone of treatment over time. Diversity measures including species richness, Simpson’s and Shannon’s indices, and species evenness were calculated from operational taxonomic unit results for each well at each sampling point in order to better understand changes in the bacterial community. Species richness tended to be higher at wells further away from the biosparging line, while diversity and evenness varied throughout the area. Correlations between PCP concentration, operational taxonomic units, and distance from biosparging wells were determined by Pearson’s product-moment correlation and Spearman’s rank correlation. Positive correlations were found between distance from biosparging wells and PCP concentration, species richness and distance, and to a smaller degree, diversity and distance. Biosparging remediation has a significant impact on the types of PCP-degrading bacteria within the groundwater matrix, and installations of this type of treatment should be applied to maximize the use of the native bacteria to assist in degradation of the contaminant.

Doctor of Philosophy / Department of Plant Pathology / Ari Jumpponen / Megan Kennelly / Soil microbial communities play fundamental and complex roles in the productivity of agriculture. However, we still have a limited understanding of the response of microbial communities to different farming systems, such as organic and conventional fertility management regimens. We applied high-throughput sequencing to develop a better understanding of how soil microbial communities (bacteria and fungi) in vegetable production respond to organic or conventional soil fertility management. Specifically, my three studies examined the following questions: 1. How do soil microbial communities from cDNA and DNA samples compare in organic and conventional fertility treatments? 2. How do soil microbial communities in a tomato cropping season respond to long-term organic vs. conventional soil fertility treatments? 3. How do soil bacterial and fungal communities respond to high tunnels, plastic mulch and organic amendments across a tomato cropping season? The first two questions were addressed at the Kansas State University Horticulture and Extension Center in Olathe, KS, using organic and conventional field plots with three levels of fertilizer. We sampled the plots during the development of a tomato crop. The third question was addressed at a commercial farm in Lawrence, KS, during its transition to organic vegetable production, during a tomato crop. The Lawrence experiment included as treatments field plots versus high tunnels, and three organic nutrient amendments. We used 454-pyrosequencing of bacterial and fungal ribosomal markers to compare total resident (DNA) and active microbial communities (cDNA, which is DNA synthesized from a single stranded RNA template) for our first question. We used Illumina MiSeq metabarcoding of bacterial and fungal ribosomal markers for our second and third questions. In all three studies we evaluated bacterial and fungal community responses using Simpson´s diversity index, Simpson´s evenness and richness for each experiment. For the first question, when we compared DNA and cDNA, bacterial diversity was higher in cDNA samples from organic compared to conventional management. In addition, fungal diversity from cDNA samples was higher than from DNA samples. In contrast, in the second question, bacterial and fungal diversity indices did not differ in the tomato crop under organic and conventional management systems. For our third question, high tunnels did not affect bacterial or fungal diversity. Use of plastic mulch for a tomato crop in open field plots did not affect bacterial richness, but decreased fungal richness compared to open field plots without plastic mulch. High-throughput sequencing provides a new perspective on the structure and dynamics of these communities. Information from this approach will ultimately improve our ability to manage soil for sustainable productivity by promoting beneficial microorganisms and suppressing pathogenic ones.

Deep subsurface evaporites are common terrestrial deep subsurface environments found globally. These deposits are known to host communities of halophilic organisms, some of which have been suggested to be millions of years old. The discovery of evaporite minerals on Mars has led to these environments becoming of interest to astrobiology, particularly because the subsurface of Mars represents the best chance of finding more clement conditions conducive to life. Despite this interest, deep subsurface evaporites remain poorly understood and we have little insight into how different salts shape the Earth's biosphere, much of which is underground. This thesis addresses several knowledge gaps present in the literature by sampling a selection of brine seeps and rock salt samples taken from Boulby Potash Mine, UK. The origin and evolution of the brines is determined with geochemical techniques, showing the majority to have been sourced from an aquifer above where they were intersected in the mine. These brines appear to have taken a variety of pathways through the subsurface leading to the presence of a range of different ions dissolved within them. The majority are Na/Cl dominated, whilst one is K/Cl dominated. One brine appears to have a different origin and probably interacted with dolomite becoming very concentrated in Mg. This variety in brine origins and migration pathways has impacted the habitability of the brines. Physicochemical measurements for chaotropicity, water activity and ionic strength, combined with culturing experiments suggest brines from the Sherwood Sandstone were habitable, but the brine from a distinct unknown source was uninhabitable. DNA was successfully extracted from three of the habitable brines and their metagenomes sequenced. These revealed communities largely functionally and phylogenetically similar to surface near saturation brines, indicating that the structure of the communities present in saturated Na/Cl brines are controlled almost exclusively by these ions rather than any other environmental difference between the surface and subsurface. Organisms were also taken from these brines and culturing experiments carried out to determine if any carbon sources were present in ancient salt that might promote growth in the absence of other carbon sources. Controls showed that the geochemical changes to the growth media induced by solving the salts, particularly sylvinite, were responsible for the increases in growth observed, indicating certain salt minerals effectively fertilise the growth of halophiles. Culturing on hydrocarbon seeps collected in the mine suggested they may provide a carbon source periodically to some organisms within the deposit. Work was done to show the presence of dissimilatory sulphate and iron reducing halophiles. Overall this significantly advances our understanding of how salts shape the Earth's biosphere, particularly its deep subsurface component, and what functional capabilities life has to persist in these environments. This work provides a new window on the potential habitability of deep subsurface extraterrestrial environments and how we might go about investigating these environments for habitable conditions.

Difficulties associated with the study of microbial communities, such as low proportions of cultivable species, have been addressed in recent years with the advent of a range of sequencing technologies and bioinformatic tools. This is enabling previously unexplored communities to be characterised and utilised in a range of biotechnology applications. In this thesis bioinformatic methods were applied to two datasets of biotechnological interest: microbial communities found living with the oil-producing alga Botryococcus braunii and microbial communities in acid mine drainage (AMD). B. braunii is of high interest to the biofuel industry due to its ability to produce high amounts of oils, in the form of hydrocarbons. However, a number of factors, including low growth rates, have prevented its cultivation on an industrial scale. Studies show B. braunii lives in a consortium with numerous bacteria which may influence its growth. This thesis reports both whole genome analysis and 16S rRNA gene sequence analysis to gain a greater understanding of the B. braunii bacterial consortium. Bacteria have been identified, some of which had not previously been documented as living with B. braunii, and evidence is presented for ways in which they may influence growth of the alga, including B-vitamin synthesis and secretion systems. AMD is a worldwide problem, polluting the environment and negatively impacting on human health. This by-product of the mining industry is a problem in the South West of England, where disused metalliferous mines are now a source of AMD. Bioremediation of AMD is an active area of research; sulphur-reducing bacteria and other bacteria which can remove toxic metals from AMD can be utilised for this purpose. Identifying bacteria and archaea that are able to thrive in AMD and which also have these bioremediation properties is therefore of great importance. Metagenomic sequencing has been carried out on the microbial community living in AMD sediment at the Wheal Maid tailings lagoon near Penryn in Cornwall. From these data have been identified a diverse range of bacteria and archaea present at both the sediment surface level and at depth, including microorganisms closely related to taxa reported from metalliferous mines on other continents. Evidence has been found of sulphur-reducing bacteria and of pathways for various other bioremediation-linked processes.

Magister Scientiae (Biodiversity and Conservation Biology) - MSc (Biodiv and Cons Biol) / The human population in sub-Saharan Africa has been increasing due to decreases in mortality rates and increases in average human age; in turn increasing poverty and pressure placed on agriculture and agricultural production. However, livestock production in South Africa, and globally, is declining due to disease and parasite prevalence, lack of feed, poor breeding, marketing management, change in nutrition in both livestock and humans, rapid urbanization, encroachment on wildlife and unfavourable climatic conditions brought about by global change. One unintended consequence has been the emergence and spread of transboundary animal diseases and, more specifically, the resurgence and emergence of zoonotic disease. Zoonotic diseases are sicknesses transmissible from animals to humans, resulting from direct contact or environmental reservoirs. Previous studies have identified small-scale farmers as the group most prevalent to contracting zoonotic diseases, especially those working in a communal dispensation. Therefore, this study focused on the communal farming area of Steinkopf in the semi-arid Namaqualand region of South Africa. Steinkopf is one of the largest Act 9 areas, with communal land tenure and a mixed farming system, sheep and goats, on about 759 ha. Steinkopf is divided into two rainfall regions, the Succulent Karoo (winter rainfall region) and the Nama Karoo (summer rainfall region). This study aims to identify and characterise the bacterial microbial communities found in the topsoil layer and faecal matter (dung) within the winter and summer rainfall regions of Steinkopf communal rangeland using Next-generation sequencing. Further, the aim is to assess whether pathogenic bacteria are present within the rangeland and what their potential impact on the local farming community might be if present. A high-throughput sequencing technique (Next-generation sequencing) was used to amplify 16S rRNA targeting the V3-V4 hypervariable regions. The phylotypes produced were 37 phyla, 353 families and 634 genera of which the most abundant bacterial phyla were Planctomycetes, Firmicutes and Bacteroidetes and the most abundant genera were Gemmata, Akkermansia and Arthrobacter. Alpha diversity indices showed a variation in species diversity, evenness and richness between soil and dung samples, it shows a higher species richness, evenness and unique OTUs detected in summer soil samples and at natural water holes. Through these analysis soil samples were regarded as superior to dung samples within this particular environment and for this particular study. Natural water holes were identified as a safer option when compared to man-made water holes as there are natural systems in place that combat the spread and growth of harmful bacterial microbes. It was found that seasonality has a great impact on the development and growth of environmental bacterial microbiota and that the current randomness of grazing routes and migrations within the Steinkopf communal rangeland is not a detriment but instead acts as a benefits to environmental and livestock health. Furthermore, a total of three pathogenic bacteria were identified however, they occurred at relatively low abundances. It can thus be concluded that this study thoroughly describes the usefulness of using a high-throughput sequencing technique such as Next-generation sequencing when amplifying a small sample size in order to achieve a large volume of information; and that currently the Steinkopf communal rangeland is not subjected to or at risk of a potential zoonotic threat.

All organisms within a forested system play a role in the biogeochemical cycle, not only within the forest but also within the global community. Soil microorganisms are a vital part of this cycle, as they sequester or make nutrients available for the development of the forest environment. When a disturbance event occurs, changes to the environment occur; however, it is unclear how these changes affect the soils microbial community. This 2-year (2007 and 2008) study was carried out to obtain a preliminary assessment of the microbial community structure and nutrient (nitrogen and phosphorus) availability within lodgepole pine stands of the Boreal Plain ecozone in west-central Alberta. Six stands of different ages were selected to determine the differences between pre and post harvest. Nutrient flux measurements were conducted using plant root simulator (PRS) probes to investigate the changes in nutrient availability. The microbial community structures were determined using two biochemical methods. The first one was a community level physiological profile (CLPP), which provides information concerning the functional characteristics of the microbial communities. Phospholipid fatty acid (PLFA) analysis provides information about the physiological characteristics of the microbial community. Analysis of the PRS probes results varied for the two nutrients: phosphorus (P) and nitrogen (N). Nitrogen availability was determined by examining the fluxes of ammonium and nitrate to the PRS probes. These did not show a strong relationship between the different aged stands during 2007 or 2008. In addition, no statistical difference was shown between the 2007 and 2008 data compared to the LFH or the mineral soil of the stands. Phosphorus, however, did show a potential trend where there was an initial increase of available P after harvest and then a gradual decrease, as the forest stands matured. This was strongly observed within the LFH, while there was a slight increase in the mineral layer. These trends remained consistent over the two-year period showing a gradual decrease in P flux to the PRS probes as a stand aged even in just one year. The microbial communities did not show a strong change after a forest-harvesting event. When examining the functional groups, there was a drastic shift in the LFH layer microbial community over the first sampling season. This change remained the same within the beginning of the second sampling year. This shift occurred in all stands due to an environmental factor, which was suspected to be the increase in moisture during the season. The change in the microbial communities was not observed, however, in the mineral layer of the soil when the functional structure was examined. When the physiological composition of the microbial communities was observed, though, using PLFA, it was apparent that the physiological characteristics of the microbial community had changed in the mineral soil. Furthermore, no physiological change was observed in the microbial communities of the LFH, only a functional change.

All organisms within a forested system play a role in the biogeochemical cycle, not only within the forest but also within the global community. Soil microorganisms are a vital part of this cycle, as they sequester or make nutrients available for the development of the forest environment. When a disturbance event occurs, changes to the environment occur; however, it is unclear how these changes affect the soils microbial community. This 2-year (2007 and 2008) study was carried out to obtain a preliminary assessment of the microbial community structure and nutrient (nitrogen and phosphorus) availability within lodgepole pine stands of the Boreal Plain ecozone in west-central Alberta. Six stands of different ages were selected to determine the differences between pre and post harvest. Nutrient flux measurements were conducted using plant root simulator (PRS) probes to investigate the changes in nutrient availability. The microbial community structures were determined using two biochemical methods. The first one was a community level physiological profile (CLPP), which provides information concerning the functional characteristics of the microbial communities. Phospholipid fatty acid (PLFA) analysis provides information about the physiological characteristics of the microbial community. Analysis of the PRS probes results varied for the two nutrients: phosphorus (P) and nitrogen (N). Nitrogen availability was determined by examining the fluxes of ammonium and nitrate to the PRS probes. These did not show a strong relationship between the different aged stands during 2007 or 2008. In addition, no statistical difference was shown between the 2007 and 2008 data compared to the LFH or the mineral soil of the stands. Phosphorus, however, did show a potential trend where there was an initial increase of available P after harvest and then a gradual decrease, as the forest stands matured. This was strongly observed within the LFH, while there was a slight increase in the mineral layer. These trends remained consistent over the two-year period showing a gradual decrease in P flux to the PRS probes as a stand aged even in just one year. The microbial communities did not show a strong change after a forest-harvesting event. When examining the functional groups, there was a drastic shift in the LFH layer microbial community over the first sampling season. This change remained the same within the beginning of the second sampling year. This shift occurred in all stands due to an environmental factor, which was suspected to be the increase in moisture during the season. The change in the microbial communities was not observed, however, in the mineral layer of the soil when the functional structure was examined. When the physiological composition of the microbial communities was observed, though, using PLFA, it was apparent that the physiological characteristics of the microbial community had changed in the mineral soil. Furthermore, no physiological change was observed in the microbial communities of the LFH, only a functional change.

The Arctic is considered as a focal region in the ongoing climate change debate. The currently observed and predicted climate warming is particularly pronounced in the high northern latitudes. Rising temperatures in the Arctic cause progressive deepening and duration of permafrost thawing during the arctic summer, creating an ‘active layer’ with high bioavailability of nutrients and labile carbon for microbial consumption. The microbial mineralization of permafrost carbon creates large amounts of greenhouse gases, including carbon dioxide and methane, which can be released to the atmosphere, creating a positive feedback to global warming. However, to date, the microbial communities that drive the overall carbon cycle and specifically methane production in the Arctic are poorly constrained. To assess how these microbial communities will respond to the predicted climate changes, such as an increase in atmospheric and soil temperatures causing increased bioavailability of organic carbon, it is necessary to investigate the current status of this environment, but also how these microbial communities reacted to climate changes in the past. This PhD thesis investigated three records from two different study sites in the Russian Arctic, including permafrost, lake shore and lake deposits from Siberia and Chukotka. A combined stratigraphic approach of microbial and molecular organic geochemical techniques were used to identify and quantify characteristic microbial gene and lipid biomarkers. Based on this data it was possible to characterize and identify the climate response of microbial communities involved in past carbon cycling during the Middle Pleistocene and the Late Pleistocene to Holocene. It is shown that previous warmer periods were associated with an expansion of bacterial and archaeal communities throughout the Russian Arctic, similar to present day conditions. Different from this situation, past glacial and stadial periods experienced a substantial decrease in the abundance of Bacteria and Archaea. This trend can also be confirmed for the community of methanogenic archaea that were highly abundant and diverse during warm and particularly wet conditions. For the terrestrial permafrost, a direct effect of the temperature on the microbial communities is likely. In contrast, it is suggested that the temperature rise in scope of the glacial-interglacial climate variations led to an increase of the primary production in the Arctic lake setting, as can be seen in the corresponding biogenic silica distribution. The availability of this algae-derived carbon is suggested to be a driver for the observed pattern in the microbial abundance. This work demonstrates the effect of climate changes on the community composition of methanogenic archae. Methanosarcina-related species were abundant throughout the Russian Arctic and were able to adapt to changing environmental conditions. In contrast, members of Methanocellales and Methanomicrobiales were not able to adapt to past climate changes. This PhD thesis provides first evidence that past climatic warming led to an increased abundance of microbial communities in the Arctic, closely linked to the cycling of carbon and methane production. With the predicted climate warming, it may, therefore, be anticipated that extensive amounts of microbial communities will develop. Increasing temperatures in the Arctic will affect the temperature sensitive parts of the current microbiological communities, possibly leading to a suppression of cold adapted species and the prevalence of methanogenic archaea that tolerate or adapt to increasing temperatures. These changes in the composition of methanogenic archaea will likely increase the methane production potential of high latitude terrestrial regions, changing the Arctic from a carbon sink to a source. / Die Arktis ist in den gegenwärtigen Diskussionen zum Klimawandel von besonderem Interesse. Die derzeitig beobachtete globale Erwärmung ist in den hohen nördlichen Breiten besonders ausgeprägt. Dies führt dazu, dass ehemals gefrorene Böden zunehmend tiefer auftauen und daher im Boden enthaltene Kohlenstoffquellen für die mikrobielle Umsetzung und Mineralisierung zur Verfügung stehen. Aufgrund dieser Prozesse entstehen klimarelevant Gase, darunter Kohlendioxid und Methan, die aus den Böden und Sedimenten freigesetzt werden können. Wenn man bedenkt, dass in den nördlichen Permafrostgebieten die Hälfte des weltweit unter der Bodenoberfläche gelagerten Kohlenstoffs gelagert ist, wird die Bedeutung dieser Region für das Verständnis des globalen Kohlenstoffkreislaufes und der möglichen Treibhaus-gasemissionen sichtbar. Trotz dieser Relevanz, sind die am Kohlenstoffumsatz beteiligten Mikroorganismen in der Arktis wenig untersucht und ihre Anpassungsfähigkeit an die gegenwärtigen Klimaveränderungen unbekannt. Die vorliegende Arbeit untersucht daher, wie sich Klimaveränderungen in der Vergangenheit auf die Anzahl und Zusammensetzung der mikrobiellen Gemeinschaften ausgewirkt haben. Dabei liegt ein besonderer Fokus auf die methanbildenden Archaeen, um das Verständnis der mikrobiellen Methandynamik zu vertiefen. Im Rahmen dieser Arbeit wurden drei Bohrkerne aus zwei verschiedenen Standorten in der russischen Arktis untersucht, darunter terrestrischer Permafrost und Seesedimente aus Sibirien und Chukotka, Russland. Mittels der Identifikation und Quantifizierung von mikrobiellen Genen und charakteristischen Bestandteilen der mikrobiellen Zellmembran war es möglich, fossile mikrobielle Gemeinschaften in Seesedimenten mit einem Alter von bis zu 480 000 Jahren und in Permafrostablagerungen mit einem Alter von bis zu 42 000 Jahren zu rekonstruieren. Es wurde gezeigt, dass es während vergangener warmen Perioden zu einem Wachstum von Bakterien und Archaeen in allen untersuchten Standorten gekommen ist. Dieser Trend konnte auch für die Gemeinschaft der methanogenen Archaeen gezeigt werden, die während warmen und insbesondere feuchten Klimabedingungen in großer Anzahl und Diversität vorhanden waren, was wiederrum Rückschlüsse auf mögliche Methanemissionen erlaubt. In den terrestrischen Permafroststandorten wird der Temperaturanstieg als direkte Ursache für die gefundene Reaktion der mikrobiellen Gemeinschaft vermutet. Im Gegenzug dazu, führte der Temperaturanstieg im untersuchten arktischen See wahrscheinlich zu einer erhöhten Primärproduktion von organischem Kohlenstoff, die wiederum das Wachstum der Mikroorganismen antrieb. Weiterhin konnte im Rahmen dieser Arbeit gezeigt werden, dass Methanosarcina-verwandte Spezies in der Russischen Arktis weit verbreitet sind und sich an veränderte Umweltbedingungen gut anpassen können. Im Gegensatz dazu stehen Vertreter von Methanocellales und Methano-microbiales, die nicht in der Lage sich an veränderte Lebensbedingungen anzupassen. Im Rahmen dieser Arbeit konnte erstmalig gezeigt werden, dass es in früheren Warmphasen zu einem vermehrten Wachstum der an der Umsetzung des organischen Kohlenstoffs beteiligten Mikroorganismen in der Russischen Arktis gekommen ist. Im Zusammenhang mit der zukünftigen Erwärmung der Arktis kann also von einer Veränderung der am Kohlenstoffkreislauf beteiligten Mikroorganismen ausgegangen werden kann. Mit den steigenden Temperaturen werden sich einige Vertreter der methanproduzierenden Mikroorganismen an die veränderten Bedingungen anpassen können, während Temperatur-empfindliche Vertreter aus dem Habitat verdrängt werden. Diese Veränderungen in der mikrobiellen Gemeinschaft können die Methanproduktion der hohen noerdlichen Breiten erhoehen und dazu beitragen, dass aus der Arktis als eine Kohlenstoffsenke eine Kohlenstoffquelle wird.

Restoration of resilient plant communities in response to environmental degradation is a critical task, and a changing climate necessitates the introduction of plant communities adapted to anticipated future conditions. Ecotypes of dominant species can affect associated organisms as well as ecosystem function. The extent of ecotypic variation in dominant tallgrass prairie species and the consequences of this variation for ecosystem functioning were studied by manipulating two potential drivers of plant community dynamics: climate and the soil microbial community. Climate was manipulated indirectly through the use of reciprocal restorations across a rainfall gradient where regional sources of dominant grasses Andropogon gerardii and Sorghastrum nutans were seeded with 8 other native species that occur in tallgrass prairie. Four dominant grass sources (originating from central Kansas [CKS], eastern Kansas [EKS], southern Illinois [SIL], or a mixture of these) were reciprocally planted within four sites that occurred across a precipitation gradient in western KS (Colby, KS), CKS (Hays, KS), EKS (Manhattan, KS) and SIL (Carbondale, IL). The three grass sources and mixture of sources were sown into plots according to a randomized complete block design at each sites (n=16, 4 plots / block at each site). Aboveground net primary productivity (ANPP) was measured at the end of the 2010 and 2011 growing season at each site. In 2010, total ANPP declined from western to eastern Kansas, but increased across the geographic gradient in 2011. The dominant grasses did not comprise the majority of community ANPP in WKS, CKS or SIL in either year but did contribute most to total ANPP at the EKS site in 2011. In 2010, volunteer forbs comprised the largest proportion of ANPP in WKS, whereas and in both years planted forbs comprised the largest proportion of ANPP in SIL. Ecotypic variation in ANPP of A. gerardii was not evident, but Sorghastrum nutans ANPP exhibited a site by source effect in 2010 that did not suggest a home site advantage. Variation in the competitive environment at each site may have masked ecotypic variation during community assembly. Further, ANPP responses suggest that grasslands in early stages of establishment may respond more stochastically to climatic variation than established grasslands. Longer term studies will clarify whether ecotypes of dominant prairie grasses affect ecosystem function or community trajectories differently during restoration. Ecotypes of dominant species may support different soil microflora, potentially resulting in plant-soil feedback. A second experiment tested for local adaptation of prairie plant assemblages to their soil microbial community. Native plant assemblages from Kansas and Illinois were tested for local adaptation to their `home' soil by reciprocally crossing soil and plant source in a greenhouse experiment. Seeds and soil were obtained from two remnant prairies, one in eastern Kansas and one in central Illinois, with similar species composition but differing climate. Seeds of four species (Andropogon gerardii, Elymus canadensis, Lespedeza capitata, Oligoneuron rigidum) common to both locations were collected, germinated, and transferred to pots to create 4-species assemblages from each region. Non-prairie (NP) soil from the edge of an Illinois agricultural field was also included as an inoculum treatment to increase relevance to restoration. Kansas and Illinois plant assemblages were subjected to a fully factorial combination of soil inocula [with associated microbial communities] (3 sources: KS, IL, NP) and soil sterilization treatment (sterilized or live). Plants were harvested after 20 weeks and soil was analyzed for microbial composition using phospholipid fatty acid (PLFA) markers. Soil sources had different nutrient concentrations and sterilization resulted in a flush of NH4+, which complicated detection of soil microbial effects. However, plant sources did exhibit variation in productivity responses to soil sources, with Kansas plants more responsive to live soil sources than Illinois plants. Despite confounding variation in soil fertility, soil inoculation was successful at manipulating soil microbial communities, and plant sources responded differently to soil sources. Consideration of feedback between soil and plants may be a missing link in steering restoration trajectories.