Academic literature on the topic 'Microbial Restoration Ecology'

Microorganisms have critical roles in the functioning of soil in nutrient cycling, structural formation, and plant interactions, both positive and negative. These roles are important in reestablishing function and biodiversity in ecosystem restoration. Measurement of the community indicates the status of the system in relation to restoration targets and the effectiveness of management interventions, and manipulation of the community shows promise in the enhancement of the rate of recovery of degraded systems.

ABSTRACT Wetland mitigation is implemented to replace ecosystem functions provided by wetlands; however, restoration efforts frequently fail to establish equivalent levels of ecosystem services. Delivery of microbially mediated ecosystem functions, such as denitrification, is influenced by both the structure and activity of the microbial community. The objective of this study was to compare the relationship between soil and vegetation factors and microbial community structure and function in restored and reference wetlands within a mitigation bank. Microbial community composition was assessed using terminal restriction fragment length polymorphism targeting the 16S rRNA gene (total bacteria) and the nosZ gene (denitrifiers). Comparisons of microbial function were based on potential denitrification rates. Bacterial community structures differed significantly between restored and reference wetlands; denitrifier community assemblages were similar among reference sites but highly variable among restored sites throughout the mitigation bank. Potential denitrification was highest in the reference wetland sites. These data demonstrate that wetland restoration efforts in this mitigation bank have not successfully restored denitrification and that differences in potential denitrification rates may be due to distinct microbial assemblages observed in restored and reference (natural) wetlands. Further, we have identified gradients in soil moisture and soil fertility that were associated with differences in microbial community structure. Microbial function was influenced by bacterial community composition and soil fertility. Identifying soil factors that are primary ecological drivers of soil bacterial communities, especially denitrifying populations, can potentially aid the development of predictive models for restoration of biogeochemical transformations and enhance the success of wetland restoration efforts.

ABSTRACTSoil microbial community characterization is increasingly being used to determine the responses of soils to stress and disturbances and to assess ecosystem sustainability. However, there is little experimental evidence to indicate that predictable patterns in microbial community structure or composition occur during secondary succession or ecosystem restoration. This study utilized a chronosequence of developing jarrah (Eucalyptus marginata) forest ecosystems, rehabilitated after bauxite mining (up to 18 years old), to examine changes in soil bacterial and fungal community structures (by automated ribosomal intergenic spacer analysis [ARISA]) and changes in specific soil bacterial phyla by 16S rRNA gene microarray analysis. This study demonstrated that mining in these ecosystems significantly altered soil bacterial and fungal community structures. The hypothesis that the soil microbial community structures would become more similar to those of the surrounding nonmined forest with rehabilitation age was broadly supported by shifts in the bacterial but not the fungal community. Microarray analysis enabled the identification of clear successional trends in the bacterial community at the phylum level and supported the finding of an increase in similarity to nonmined forest soil with rehabilitation age. Changes in soil microbial community structure were significantly related to the size of the microbial biomass as well as numerous edaphic variables (including pH and C, N, and P nutrient concentrations). These findings suggest that soil bacterial community dynamics follow a pattern in developing ecosystems that may be predictable and can be conceptualized as providing an integrated assessment of numerous edaphic variables.

SUMMARY In the past several years, we have witnessed an increased interest in understanding the structure and function of the indigenous microbiota that inhabits the human body. It is hoped that this will yield novel insight into the role of these complex microbial communities in human health and disease. What is less appreciated is that this recent activity owes a great deal to the pioneering efforts of microbial ecologists who have been studying communities in non-host-associated environments. Interactions between environmental microbiologists and human microbiota researchers have already contributed to advances in our understanding of the human microbiome. We review the work that has led to these recent advances and illustrate some of the possible future directions for continued collaboration between these groups of researchers. We discuss how the application of ecological theory to the human-associated microbiota can lead us past descriptions of community structure and toward an understanding of the functions of the human microbiota. Such an approach may lead to a shift in the prevention and treatment of human diseases that involves conservation or restoration of the normal community structure and function of the host-associated microbiota.

This study examined the rehabilitation potential of AM fungi with organic and inorganic fertilisers under pot and field trial conditions as well as their interaction with rhizospheric organisms and specific functional groups. In addition, the study highlighted the effects of land-use management on AM fungal populations in soil and the mycorrhizal status of some selected plants from one of the study sites. The study focussed on two sites that differ in operational activities and these included a mined area that was to be rehabilitated and a commercial farming site. A pot trial was conducted using an overburdened soil resulting from kaolin clay mining. Pots were seeded with Cynodon dactylon and treated with either Organic Tea or NPK (3:1:5) fertiliser, with or without AM fungal inoculum. The compatibility of these fertilisers with AM fungi was assessed by plant growth and percentage root colonisation. Maximum shoot height and plant biomass were observed at the 28th week with NPK (3:1:5) fertiliser supporting mycorrhizal colonisation by 80%. The result indicated the potential of AM fungi to be used in rehabilitation with minimal phosphate fertiliser. Similarly, a field trial was set-up using 17 x 17 m[superscript 2] plots in the mining site that were treated with the same organic and inorganic fertilisers as well as with AM fungal inoculum in different combinations. The interaction between AM fungi and soil microbial population was determined using culture dependent and culture independent techniques. The culture dependent technique involved the use of soil dilution and plating on general purpose and selective media. The result showed that there was no change in the total culturable bacterial number in the untreated and AM fungal treated plots, while a change in species composition was observed in the functional groups. Different functional groups identified included nitrogen fixing bacteria, pseudomonads, actinomycetes, phosphate solubilisers and the fungal counterparts. Gram-positive bacteria were observed as the predominant phenotypic type, while nitrogen fixers and actinomycetes were the predominant functional groups. Species identified from each functional group were Pseudomonas fulva, Bacillus megaterium, Streptomyces and actinomycetales bacteria. Meanwhile, fungi such as Ampelomyces, Fusarium, Penicillium, Aspergillus, Cephalosporium and Exserohilium were identified morphologically and molecularly. Furthermore, the mining site had a significantly higher bacterial number than the farming site thereby indicating the effects of land-use management on culturable bacterial numbers. The culture independent technique was carried out by cloning of the bacterial 16S rDNA and sequencing. Identified clones were Bradyrhizobium, Propionibacterium and Sporichthya. A cladogram constructed with the nucleotides sequences of identified functional species, clones and closely related nucleotide sequences from the Genbank indicated that nucleotide sequences differed in terms of the method used. The activity and establishment of the introduced AM fungal population was determined by spore enumeration, infectivity assay, percentage root colonisation and assessment of glomalin concentrations. The results indicated that the two land use types affected AM fungal populations. However, the establishment of AM fungi in the farming site was more successful than in the mining site as indicated by the higher infectivity pontential. Selected host plants, which were collected around the mine area, were observed to be mainly colonised by AM fungi and these were identified as Pentzia incana, Elytropappus rhinocerotis, Euphorbia meloformis, Selago corymbosa, Albuca canadensis and Helichrysum rosum. These plant species were able to thrive under harsh environmental conditions, thereby indicating their potential use as rehabilitation host plants. Generally, the findings of this study has provided an insight into the interaction between arbuscular mycorrhizal fungi and other soil microorganisms in two fields with differing land use management practices.

Differences in microbial function via extracellular enzyme activity (EEA) were investigated to determine the potential effects of hydrology and plant-soil-microbe interactions in a young non-tidal freshwater riparian wetland. To study these relationships, three plots were established along a moisture gradient (Wet, Intermediate, Dry) within VCU Rice Center Within each main plot, five subplots were left undisturbed while another five were cleared of all above-ground plant biomass. Homogenized soil cores (top 10 cm) were analyzed for pH, redox, C:N, soil organic matter (SOM) content, saturation, and temperature. Microbial function was assessed using extracellular enzyme analysis. For most enzymes, a site difference was observed due to soil moisture content, which had an effect on soil pH, redox potential, and plant community composition. For most extracellular enzymes the presence of vegetation was associated with higher activity. It is important to note that reestablishing native hydrologic and vegetated conditions are paramount in achieving previous functionality.

Thesis (MSc (Conservation Ecology and Entomology))--University of Stellenbosch, 2009.
ENGLISH ABSTRACT: Much of South African lowland fynbos vegetation has been transformed by agriculture and invasive alien grass species. The artificial reduction of plant available N and P levels in soils, through the addition of carbon and calcium respectively, may provide a means of retarding the growth of alien grasses stimulated by soil nutrient enrichment. Furthermore, the competitive advantage of native lowland fynbos species adapted to nutrient impoverished soils may be increased by these additions. The above premise was tested in both field- and greenhouse-based trials by applying systemic and contact herbicides to reduce the large alien invasive grass biomass. This was followed by the addition of C as sucrose and Ca as gypsum to reduce plant available N and P respectively in the soils. The effects of these combined herbicide and soil nutrient amendment treatments on plant physiology and growth were examined in both resident alien and indigenous species and in several herbaceous and woody native species introduced as seeds and seedlings. Also, soils sampled from the different treatments in both trials were chemically analyzed. There was a total absence of seedling recruitment from seeds of all 9 indigenous species sown into soils in the field-based trial while introduced juveniles of another 9 indigenous species displayed a high mortality during the dry summer season. These detrimental effects were less severe in the greenhouse-based trial which received more regular watering and where successful seedling recruitment from seeds sown occurred in four indigenous species. Sucrose additions, both exclusively and in combination with gypsum, caused significant reductions in foliar chlorophyll, photosystem II (PSII) function and above-ground biomass of most resident and introduced alien and indigenous species. These reductions were less prominent where herbicides were applied, a possible consequence of N and P supplementation of soils by the decomposing plant biomass. This was supported by the elevated soil K, Na and N concentrations measured in soils where contact and systemic herbicides were applied. However, no significant changes in soil N or P were apparent following sucrose and gypsum additions respectively, the latter attributed to the acidic soils which precluded the formation of insoluble P complexes. A second study tested the hypothesis that exogenous sucrose addition to soils inhibits plant growth by stimulating soil microbial biomass which accumulates soil nitrogen rendering it unavailable to plants. Two native, early seral species (Dimorphotheca pluvialus (L.) Moench and Ursinia anthemoides (L) Poir. subsp anthemoides) were cultured in heat sterilized (2200C for 72 hours) and non-sterilized soils in a greenhouse under four different levels of sucrose (0, 100, 200 and 300 g m-2) supplied monthly over a four-month active growing period. Foliar chlorophyll iii contents, photosystem II (PSII) efficiencies, shoot and root lengths and dry mass, inflorescence numbers and N and P contents were measured in the plants, and N and P contents and bacterial cell and coliform numbers analyzed in the soils. Both D. pluvialis and U. anthemoides displayed significant reductions in PSII efficiency, chlorophyll content, accumulation of biomass and N and P in response increased levels of sucrose, which initially seemingly supported the hypothesis as these reductions were of substantially greater magnitude in plants cultivated in non-sterilized than sterilized soils. Despite this, there was no evidence of any significant increases in bacterial and coliform cell numbers in response to increased levels of sucrose supplied or any significant reductions in soil N and P contents following sucrose additions in both sterile and non-sterilized soils. Greater numbers of bacteria and coliforms were measured in sterilized than non-sterilized soils which corresponded with reduced soil N contents but these were not reflected in like changes in plant PSII efficiency and growth and total amounts of N taken up by plants which displayed massive increases in sterilized soils. The findings did not support the hypothesis and pointed to an abiotic mechanism of sucrose inhibition of plant photosynthesis and growth. The study concludes that the suitability of adding sucrose and gypsum to degraded renosterveld ecosystem soils to promote the competitiveness of native taxa against alien grasses is dubious. Other restoration alternatives such as natural re-colonization, transfer of soils containing viable seeds from pristine communities and top soil removal should be considered.
AFRIKAANSE OPSOMMING: Baie van Suid Afrika se laagland fynbos plantegroei is verander deur landbou en uitheemse indringer grasspesies. Die kunsmatige reduksie van plantbeskikbare N en P vlakke in die grond deur die toevoeging van koolstof en kalsium onderskeidelik, kan ’n metode wees om die groei van indringer grasse te vertraag, wat gestimuleer word deur grondvoedingstofverryking. Die kompeterende voordeel van die inheemse laagland fynbosspesies wat aangepas is tot voedingstofarme grond kan verhoog word deur die toevoegings. Bogenoemde postulaat is in beide die veld- en die glashuis-gebaseerde eksperimente getoets deur die aanwending van sistemiese en kontak onkruiddoder om die groot indringer grasbiomassa te verminder gevolg deur die byvoeging van C as sukrose en Ca as gips om die plantbeskibare N en P onderskeidelik te verminder in die grond. Die effekte van die gekombineerde onkruiddoder en grondvoedingstof verbeteringsbehandelings op die fisiologie en groei van die plante is ondersoek in beide inheemse- en residente indringerspesies asook in verskeie kruidagtige- en houtagtige inheemse spesies wat aangeplant was as sade en saailinge. Grondmonsters van die verskillende behandelings in beide studies was versamel en was chemies geanaliseer. Daar was ’n definitiewe afwesigheid van nuwe saailinge van sade van al nege indringerspesies wat gesaai was in grond in die veldgebaseerde studie, en saailinge van nog nege inheemse spesies het ’n hoë mortaliteit getoon gedurende die droë somerseisoen. Hierdie skadelike effekte was minder ernstig in die glashuisgebaseerde studie wat meer benat was, en waar nuwe saailinge suksesvol geproduseer was deur sade in vier inheemse spesies. Sukrose byvoegings, beide uitgesluit en in kombinasie met gips, het ’n afname in blaarchlorofil, fotosisteem II en bogrondse biomassa van die meeste van die residente en aangeplante indringer- en inheemse spesies getoon. Hierdie afnames was minder prominent waar onkruiddoder aangewend was, ’n moontlke oorsaak van N en P aanvulling van grond deur die verrottende plantbiomassa. Dit word ondersteun deur verghoogde grond K, Na en N konsentrasies, gemeet in grond waar kontak en sistemiese onkruiddoder toegevoeg was. Geen noemenswaardige veranderinge in grond N of P was sigbaar na byvoeging van sukrose en gips onderskeidelik nie. Laasgenoemde het bygedra tot suuragtige grond wat die formasie van onoplosbare P komplekse verkom het. ‘n Tweede studie het die hipotese getoets waar eksogene sukrose byvoeging tot grond plantegroei inhibeer deur die grond mikrobe biomassa te stimuleer wat akkumuleer wat in grond stikstof en dit nie beskikbaar maak vir plante nie.Twee inheemse vroeë intermediêre stadium spesies (Dimorphotheca pluvialus (L.) Moench en Ursinia anthemoides (L) Poir. subsp v anthemoides) was gekweek in hitte gesteriliseerde grond (2200 C vir 72 uur) en in nie-gesteriliseerde grond in ’n glashuis onder vier verskillende vlakke van van sukrose (0, 100, 200 en 300 g m-2) bygevoeg maandeliks oor ‘n 4 maande aktiewe groei periode. Blaarchlorofilinhoud, fotosisteem II (FS II) doeltreffendheid, groeipunt en wortel lengte en droë massa, blomgetalle en N en P inhoud was gemeet in die plante sowel as N en P inhoud en bakteriële sel en kolivorm getalle was geanaliseer in die grond. Beide D. pluvialis en U . anthemoides het ’n afname getoon in FS II doeltreffendheid, chlorofilinhoud, biomassa akkumulasie, N en P response op verhoogde vlakke van sukrose, wat aanvanklik aangetoon het dat dit die hipotese ondersteun want hierdie afnames wat heelwat groter in plante wat gekweek was in ongesteriliseerde grond as in gesteriliseerde grond. Daar was geen toename in baketriële en kolivorm sel getalle in rssponse tot verhoogde vlakke van sukrose byvoegings of enige noemenswaardige in grond N en P inhoud na byvoeging van sukrose in beide steriele en nie-steriele grond nie. Groot getalle bakterieë en kolivorme was gemeet in gesteriliseerde grond as in ongesteriliseerde grond. Dit korrespondeer met verminderde grond N inhoud maar dit was nie gereflekteer in veranderinge in plant FS II doeltreffendheid, groei en die totale hoeveelhede N wat opgeneem was deur plante wat ’n massiewe toename getoon het ongesteriliseerde grond nie. Hierdie bevindings het nie die hipotese ondersteun nie en het gewys na ’n abiotiese meganisme van sukrose inhibisie van plant fotosintese en groei. Die studie lei dus af dat die geskiktheid om sukrose en gips by te voeg tot gedegradeerde renosterveld ekosisteemgrond om kompetisie tussen inheemse plante en indringer grasse te promoveer, twyfelagtig is. Ander restorasie alternatiewe soos natuurlike herkolonisasie, oordrag van grond wat lewensvatbare sade bevat van onbeskadigde gemeenskappe en bogrond verwydering word oorweeg.

[Truncated abstract] Recovery of soil nutrients, microbial populations and carbon (C) and nitrogen (N) cycling processes are critical to the success of rehabilitation following major ecosystem disturbance. Bauxite mining represents a major ecosystem disturbance to the jarrah (Eucalyptus marginata) forest in the south-west of Western Australia. Mining has created a mosaic of mined areas in various stages of succession surrounded by non-mined forest areas. Initial site preparations within rehabilitation areas such as contour ripping alter soil structure (creation of mound and furrows) and over time also influence the distribution of vegetation and litter. Current performance criteria developed by industry, government and other stakeholders have determined that before post-bauxite mined areas of jarrah forest can be integrated back into normal forest management practises they should be functional and demonstrate resilience to normal forest disturbances such as fire. Furthermore, resilience should be of a manner comparable to non-mined analogue forest sites. Currently little is known of the resilience of microbial communities and C and N cycling in rehabilitation sites to normal forest disturbances such as prescription burning. As such, before rehabilitated jarrah forests can be successfully integrated into broad scale forest management regimes, a more thorough knowledge of the potential impacts of burning practises on the soil microbial community and C and N cycling processes in these systems is required. ... While there are similar rates of C and N cycling the underlying microbial community structure was distinctly different; implying a high degree of functional redundancy with respect to C and N cycling. Differences in the C and N cycling and structure of the microbial communities were likely to be due to differences in soil environmental conditions (i.e. soil alkalinity/acidity, soil moisture) and C substrate availability which influence the physiological status of the microbial community and in turn are related to successional age of the forests. Results also suggest that the measurement of CLPP can be a useful approach for assessment of changes in the functional ability of microbial communities. However, the interpretation of how well these rehabilitation forests have recovered heterotrophic abilities was greatly affected by the methodological approach used (e.g. MicroRespTM or Degens and Harris, 1997). Importantly, results from Chapter 4 and 5 suggested that the effects of a moderate prescription fire on C and N processes, CLPP and microbial community structure of 18 year old rehabilitation forests are likely to be short-lived (< 2 years). Furthermore, the effects of the moderate spring prescription fire were not large enough to decouple C and N cycling processes over the short-term (< 1 years) which suggests that by 18 years of age rehabilitation forests demonstrate comparable functional resilience to a moderate prescription burn.

No presente estudo perseguimos os seguintes objetivos: a) caracterizar o grau de degradação física e química de solos usados em cultivo agrícola por várias décadas, originalmente cobertos por Mata Atlântica (Floresta Estacional Semidecidual) em Botucatu, SP; b) avaliar as alterações biológicas destes solos ao longo de 16 meses pós-reflorestamento com diferentes modelos de associação de espécies da Mata Atlântica. As áreas experimentais estavam localizadas em duas propriedades (Fazenda Lageado e Edgardia) da Faculdade de Ciências Agronômicas (FCA/UNESP) em Botucatu-SP. O clima da região é do tipo tropical com inverno seco (Cwa, classif. de Köppen). Os solos das áreas experimentais são os seguintes: um Nitossolo Vermelho (NV) de textura argilosa; um Argissolo Vermelho-Amarelo (AVA) álico, de textura areia-franca; e um Latossolo Vermelho-Amarelo (LVA) álico, de textura arenosa. Seis tratamentos (delineamento em blocos casualizados, com três repetições) foram usados: Testemunha; Semeadura Direta; Taungya; Consorciação; Restauração e, por fim, Fragmentos Florestais. Os atributos físicos (textura, densidade e porosidade) foram avaliados nas camadas de 0-10, 10-20 e 20-40cm, os atributos químicos (pH, MO, P, S, K, Ca, Mg, H, Al, CTC, B, Cu, Fe, Mn e Zn) nas camadas de 0-5, 5-10, 10-20 e 20-40cm e os atributos biológicos (C da biomassa microbiana, liberação de CO2 e mineralização de N) nas camadas de 0-5 e 5-20cm. No NV, o teor de argila no solo degradado foi 57% maior do que o obtido no solo sob o Fragmento Florestal (camada 0-10cm), no AVA, 33% maior e, no LVA, 77% menor. Este efeito, no NV e AVA, foi atribuído à remoção de camadas superiores do solo, mais arenosas, pela erosão e exposição das camadas inferiores mais argilosas. No LVA, o menor teor de argila e silte no solo degradado foiatribuído à perda destas frações por eluviação ou em suspensão na enxurrada. O pH, teor de MO, de P e de Ca nos solos NV e LVA foram bem superiores nos Fragmentos Florestais relativamente aos obtidos nas áreas com solos degradados. Diferenças menos acentuadas foram observadas no AVA, como também detectadas para a composição textural, indicando que este solo está menos degradado que os demais. A CTC dos solos mostrou-se altamente correlacionada com os teores de argila e de MO. Isto destaca a importância da preservação da composição granulométrica e elevação dos teores de MO com o intuito de restaurar importantes propriedades físico-químicas do solo, como a CTC. Em áreas com cobertura florestal (Fragmentos Florestais do NV, AVA e LVA), o C da biomassa microbiana apresenta maiores valores na camada superficial e no verão. Fato atribuído a condições mais favoráveis (MO, pH, umidade, temperatura, etc) à manutenção da vida microbiana no solo. O C da biomassa microbiana e, em menor escala, a liberação de CO2 apresentaram-se como bons indicadores das alterações ocorridas após o reflorestamento com as diferentes associações de espécies. No LVA, como o solo desta área se apresenta mais degradado, em relação ao NV e ao AVA, a alta correlação e relação C microbiano/C orgânico indica que a biomassa microbiana é um importante compartimento de reserva do C orgânico do solo. Quanto aos atributos biológicos, as diferenças entre os Fragmentos Florestais e os demais tratamentos continuam a existir nas três áreas e camadas, devendo ser gradativo o retorno desses atributos à condição pré-existente; ademais, o tempo de retorno sofrerá influência das condições edafoclimáticas da área e da associação de espécies presentes.
This study seeks to: a) characterize the degree of physical and chemical degradation of the soils used in agricultural cultivation for several decades, originally covered by the Atlantic Forest (Seasonal Semideciduous Forest) in Botucatu, SP; b) evaluate the biological changes of these soils along a 16-month post-reforestation with different models of species association of the Atlantic Forest. The experimental areas were located in two properties (Fazenda Lageado and Edgardia) of the Agronomic Sciences College (FCA/UNESP) in Botucatu-SP. The climate in that region is the tropical type with dry winter (Cwa, Köppen class.). The soils of the experimental areas are: clayey Red Nitosol (NV), loamy alic Red-Yellow Argisol (AVA), and sandy alic Red-Yellow Latosol (LVA). Six treatments (randomized block design with three replications) were used: Test; Direct Seeding; Taungya; Consortium; Restoration and finally Forestal Fragments. The physical attributes (texture, density and porosity) were evaluated in layers of 0-10, 10-20 and 20-40cm; the chemical attributes (pH, MO, P, S, K, Ca, Mg, H, Al, CTC, B, Cu, Fe, Mn and Zn) in layers of 0-5, 5-10, 10-20 and 20-40cm and the biological attributes (Microbial biomass C, CO2 release and N mineralization) in layers of 0-5 and 5-20cm. The clay content in the degraded soil in NV was 57% higher than that obtained in soil under Forest Fragment (0-10cm layer), 33% higher in AVA, and 77% lower in LVA. This effect in NV and AVA was accredited to the removal of the soil top layers, which are sandier due to the erosion and exposition of the lower layers that are more clayey. In LVA the lowest clay and silt content in the degraded soil was accredited to the loss of these fractions by eluviation or flood suspension. The pH, MO, P and Ca contents in NV and LVA soils were much higher in Forestal iv Fragments regarding those reached in degraded soil areas. The less marking differences were observed in AVA and also detected for the textural composition, thus indicating that this soil is less degraded than the other ones. The CTC of the soils was highly correlated with the clay and MO contents. That highlights the importance of preserving the granulometric composition and elevation of the MO contents in order to restore important physical-chemical soil properties, such as the CTC. In primary forest areas (NV, AVA and LVA Forestal Fragments), the microbial biomass C presents higher values at the top layer and in the summer, a fact accredited to more favorable conditions (MO, pH, moisture, temperature, etc) for the maintenance of the microbial life in the soil. The microbial biomass C and, in a lesser scale, the CO2 release were good indicators of the changes occurred after the reforestation with the different species associations. In the LVA, since the soil of this area is more degraded in relationship to NV and AVA, the high correlation and microbial C/organic C relationship indicate that the microbial biomass is an important reserve compartment of the soil organic C. As to the biological attributes, the differences between the Forestal Fragments and the remaining treatments still exist in the three areas and layers, and the return to the pre-existing attributes is likely to be gradual; moreover, the time of return should undergo influences of the pedoclimatic conditions of the area and of the association of the present species.

abstract: Biological soil crusts (biocrusts) are topsoil communities of organisms that contribute to soil fertility and erosion resistance in drylands. Anthropogenic disturbances can quickly damage these communities and their natural recovery can take decades. With the development of accelerated restoration strategies in mind, I studied physiological mechanisms controlling the establishment of cyanobacteria in biocrusts, since these photoautotrophs are not just the biocrust pioneer organisms, but also largely responsible for improving key soil attributes such as physical stability, nutrient content, water retention and albedo. I started by determining the cyanobacterial community composition of a variety of biocrust types from deserts in the Southwestern US. I then isolated a large number of cyanobacterial strains from these locations, pedigreed them based on their 16SrRNA gene sequences, and selective representatives that matched the most abundant cyanobacterial field populations. I then developed methodologies for large-scale growth of the selected isolates to produce location-specific and genetically autochthonous inoculum for restoration. I also developed and tested viable methodologies to physiologically harden this inoculum and improve its survival under harsh field conditions. My tests proved that in most cases good viability of the inoculum could be attained under field-like conditions. In parallel, I used molecular ecology approaches to show that the biocrust pioneer, Microcoleus vaginatus, shapes its surrounding heterotrophic microbiome, enriching for a compositionally-differentiated “cyanosphere” that concentrates the nitrogen-fixing function. I proposed that a mutualism based on carbon for nitrogen exchange between M. vaginatus and its cyanosphere creates a consortium that constitutes the true pioneer community enabling the colonization of nitrogen-poor, bare soils. Using the right mixture of photosynthetic and diazotrophic cultures will thus likely help in soil restoration. Additionally, using physiological assays and molecular meta-analyses, I demonstrated that the largest contributors to N2-fixation in late successional biocrusts (three genera of heterocystous cyanobacteria) partition their niche along temperature gradients, and that this can explain their geographic patterns of dominance within biocrusts worldwide. This finding can improve restoration strategies by incorporating climate-matched physiological types in inoculum formulations. In all, this dissertation resulted in the establishment of a comprehensive "cyanobacterial biocrust nursery", that includes a culture collection containing 101 strains, isolation and cultivation methods, inoculum design strategies as well as field conditioning protocols. It constitutes a new interdisciplinary application of microbiology in restoration ecology.
Dissertation/Thesis
Doctoral Dissertation Liberal Studies 2019

abstract: Biological soil crusts (biocrust) are photosynthetic communities of organisms forming in the top millimeters of unvegetated soil. Because soil crusts contribute several ecosystem services to the areas they inhabit, their loss under anthropogenic pressure has negative ecological consequences. There is a considerable interest in developing technologies for biocrust restoration such as biocrust nurseries to grow viable inoculum and the optimization of techniques for field deployment of this inoculum. For the latter, knowledge of the natural rates of biocrust dispersal is needed. Lateral dispersal can be based on self-propelled motility by component microbes, or on passive transport through propagule entrainment in runoff water or wind currents, all of which remain to be assessed. I focused my research on determining the capacity of biocrust for lateral self-propelled dispersal. Over the course of one year, I set up two greenhouse experiments where sterile soil substrates were inoculated with biocrusts and where the lateral advancement of biocrust and their cyanobacteria was monitored using time-course photography, discrete determination of soil chlorophyll a concentration, and microscopic observations. Appropriate uninoculated controls were also set up and monitored. These experiments confirm that cyanobacterial biological soil crusts are capable of laterally expanding when provided with presumably optimal watering regime similar to field conditions and moderate temperatures. The maximum temperatures of Sonoran Desert summer (up to 42 °C), exacerbated in the greenhouse setting (48 °C), caused a loss of biomass and the cessation of lateral dispersal, which resumed as temperature decreased. In 8 independent experiments, biocrust communities advanced laterally at an average rate of 2 cm per month, which is half the maximal rate possible based on the instantaneous speed of gliding motility of the cyanobacterium Microcoleus vaginatus. In a span of three months, populations of M. vaginatus, M. steenstrupii, and Scytonema spp. advanced 1 cm/month on average. The advancing crust front was found to be preferentially composed of hormogonia (differentiated, fast-gliding propagules of cyanobacteria). Having established the potential for laterally self-propelled community dispersal (without wind or runoff contributions) will help inform restoration efforts by proposing minimal inoculum size and optimal distance between inoculum patches.
Dissertation/Thesis
Masters Thesis Biology 2017