Space, Time and Change: Investigations of Soil Bacterial Diversity and Its Drivers in the Mongolian Steppe PDF Download
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Author: Aurora A. MacRae-Crerar
Publisher:
ISBN:
Category :
Languages : en
Pages : 312
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Microorganisms are the most diverse life forms on Earth and are the foundation of any ecosystem. As estimates of microbial diversity rapidly increase with advances in sequencing technologies, so does the need to identify the drivers of such overwhelming diversity. This is particularly true in soil—the most biodiverse habitat on the planet and the key component of terrestrial ecosystems, which are being altered by changes in climate and land use. In order to understand the potential consequences of these changes, we conducted a multi-year experiment to test the effects of global change on soil bacterial communities in northern Mongolia, a region where air temperatures have increased by 1.7 °C since 1960, and traditional land-use patterns are shifting with socio-economic changes. Set in the semi-arid steppe, our global change experiment allowed as to evaluate responses to multiple stressors at once over a range of spatial and temporal scales. Over the course of three years, we investigated soil bacterial diversity at two positions (upper and lower) along a south-facing slope and documented the response of these communities to three experimental treatments: a Watering experiment (upper slope only), a Grazing experiment (lower slope only) and a Climate Manipulation experiment (both slopes). We measured diversity using both the number and abundance of distinct bacterial taxa in a soil sample and then correlated these findings with corresponding measurements of biotic and abiotic factors, which included plant richness and biomass, as well as plant available N, pH, soil moisture and soil temperature. We found that temporal and spatial factors explained much of the variation in the bacterial communities. After accounting for temporal and spatial variation, soil moisture content was the primary driver structuring bacterial diversity across the landscape and within experimental treatments. In particular, the effects of climate change on these semi-arid grasslands may act primarily through soil moisture content. Concomitant shifts in key members of the bacterial community may ultimately be bioindicators of a drier future for Mongolia.
Author: Aurora A. MacRae-Crerar
Publisher:
ISBN:
Category :
Languages : en
Pages : 312
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Book Description
Microorganisms are the most diverse life forms on Earth and are the foundation of any ecosystem. As estimates of microbial diversity rapidly increase with advances in sequencing technologies, so does the need to identify the drivers of such overwhelming diversity. This is particularly true in soil—the most biodiverse habitat on the planet and the key component of terrestrial ecosystems, which are being altered by changes in climate and land use. In order to understand the potential consequences of these changes, we conducted a multi-year experiment to test the effects of global change on soil bacterial communities in northern Mongolia, a region where air temperatures have increased by 1.7 °C since 1960, and traditional land-use patterns are shifting with socio-economic changes. Set in the semi-arid steppe, our global change experiment allowed as to evaluate responses to multiple stressors at once over a range of spatial and temporal scales. Over the course of three years, we investigated soil bacterial diversity at two positions (upper and lower) along a south-facing slope and documented the response of these communities to three experimental treatments: a Watering experiment (upper slope only), a Grazing experiment (lower slope only) and a Climate Manipulation experiment (both slopes). We measured diversity using both the number and abundance of distinct bacterial taxa in a soil sample and then correlated these findings with corresponding measurements of biotic and abiotic factors, which included plant richness and biomass, as well as plant available N, pH, soil moisture and soil temperature. We found that temporal and spatial factors explained much of the variation in the bacterial communities. After accounting for temporal and spatial variation, soil moisture content was the primary driver structuring bacterial diversity across the landscape and within experimental treatments. In particular, the effects of climate change on these semi-arid grasslands may act primarily through soil moisture content. Concomitant shifts in key members of the bacterial community may ultimately be bioindicators of a drier future for Mongolia.
Author: Jessica Furrer Chau
Publisher:
ISBN:
Category :
Languages : en
Pages : 184
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Author: Lebohang Lieketseng Lekhanya
Publisher:
ISBN:
Category :
Languages : en
Pages :
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In the past, the response of microbial populations to anthropogenic disturbances was studied using conventional methods based on cultivation of microorganisms and on measurement of their metabolic activities (Fantroussi et al., 1999). However, these culturing methods often account for a small proportion of the total microbial community (Ibekwe and Kennedy, 1998: Hill et al., 2000). To overcome this, molecular techniques were developed and these allowed for the analyses of microorganisms in their natural habitats. Analysis of the 16S rRNA molecule and its corresponding gene (16S rDNA) has been the most widely used approach in the last decade (Amman et al., 1995). Although molecular techniques based on PCR have been used to eliminate the bias of culturing methods, they also have their drawbacks (Wintzingerode et al., 1997: Kirk et al., 2004). As another alternative, Garland and Mills (1991) developed a rapid community-level physiological approach to study microbial communities. The use of the community-level approach to microorganisms provided an accurate and meaningful measure of the heterotrophic microbial community by measuring the community's metabolic abilities (Garland and Mills, 1991). Zak et al. (1994) used the method to study the functional diversity of microbial communities. The approach has been used to study the soil functional diversities in polluted or disturbed environments. Over the years, the application of gypsum in agriculture has received much attention. The gypsum has been used to ameliorate both acidic and alkali soils with elevated amounts of salinity (Suhayda et al., 1997: Sun et al., 2000). In these studies, the application of gypsum lead to changes in the soil chemical properties by causing a drastic increase in the amount of exchangeable calcium and sulphate and reduced the levels of exchangeable aluminium. It has been noted that high levels of aluminium and/or reduced amounts of calcium restrict root elongation and thus hindered the plants ability to access adequate water (Sun et al., 2000). Also, the replacement of sodium ions with calcium ions resulted in the flocculation of soil particles and improved the porous structure and water permeability of the soil (Suhayda et al., 1997). This study revealed that the application of the gypsiferous mine water did not have any negative impact on the bacterial communities. In fact, on average, the bacterial diversities were found to be higher in the gypsum-irrigated soils. This was most evident in pivot Major and Tweefontein, where the gypsum-irrigated soils were more diverse than the control soils. DGGE results from pivot Major and Tweefontein revealed a high level of bacterial diversity in gypsum-irrigated soils, as estimated by the number of dominant bands. Also, the number of heterotrophic bacteria in the gypsum-irrigated soils was one to two orders of magnitude higher than in the control soils. Principal component analysis performed on BIOLOG data showed that in both pivot Major and Tweefontein, the gypsum-irrigated soils were able to utilise a wider range of carbon sources as compared to their control counterparts. The bacterial communities in pivot Four appeared to be steady in both the gypsum-irrigated soils and the control soils. The number of visible DGGE bands was consistent between the gypsum-irrigated and the control soils. The heterotrophic bacterial counts in the gypsum-irrigated soils had an average of 273x106 cfu g-1 soil and those present in the control soils were slightly higher at 380x106 cfu g-1 soil. Principal component analysis revealed no differences in terms of substrate utilisation capabilities among the gypsum-irrigated soils and the control soils. All three techniques revealed no significant difference in community structures between soil profiles at 0-10 cm and 40-60 cm. The lack of difference could be attributed to the crops planted in all three pivots during sampling. The root system of Zea Maysplants enhanced microbial growth by exuding nutrients such as amino acids and sugars. In conclusion, the application of polyphasic approach proved successful in studying the response of soil bacterial communities to gypsiferous mine water. The use of both culture-dependent and culture-independent methods is recommended as the methods compensate each other's limitations and therefore provide a more detailed description of the community. In this study, the application of gypsiferous mine water did not have an adverse effect on the soil bacterial communities. In fact, the addition of gypsiferous mine water seemed to ameliorate the soil bacterial communities. However, further comprehensive study is needed to determine the response of bacterial communities to gypsiferous mine water over longer periods of time. 16S rDNA sequencing and analysis of DGGE bands should also be done to identify the bacterial species present in the gypsum-irrigated samples.
Author: Rama Kant Dubey
Publisher:
ISBN: 9783030155179
Category : Electronic books
Languages : en
Pages : 104
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Book Description
This book explores the significance of soil microbial diversity to understand its utility in soil functions, ecosystem services, environmental sustainability, and achieving the sustainable development goals. With a focus on agriculture and environment, the book highlights the importance of the microbial world by providing state-of-the-art technologies for examining the structural and functional attributes of soil microbial diversity for applications in healthcare, industrial biotechnology, and bioremediation studies. In seven chapters, the book will act as a primer for students, environmental biotechnologists, microbial ecologists, plant scientists, and agricultural microbiologists.--
Author: Kerri Ann Russell
Publisher:
ISBN:
Category :
Languages : en
Pages : 60
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In natural ecosystems, like deciduous and coniferous forests, soil CO2 flux or soil respiration is highly variable and influenced by multiple factors including temperature, precipitation, dissolved soil organic carbon (DOC), dissolved organic matter (DOM), and bacterial and fungal biomass and diversity. However, as the human population continues to grow rapidly, so too do urbanized landscapes with unknown consequences to soil respiration. To determine the extent urbanization influences seasonal shifts in microorganisms and environmental drivers alter soil respiration, we evaluated bacterial and fungal communities, soil physiochemical characteristics, and respiration in forested and urbanizing ecosystems in three watersheds across northern Utah, USA. Based on the next-generation sequencing of the 16s DNA and RNA, we found that montane bacteria were predominantly structured by season while urban bacteria were influenced by degree of urbanization. There was no apparent effect of season on montane fungi, but urban fungal communities followed patterns similar to urban bacterial communities. Bacterial diversity was sensitive to seasonality, especially in montane ecosystems, declining 21-34% from spring to summer and staying relatively low into fall, and fungal diversity was generally depressed in spring. Urban bacterial communities were differentiated by substantially more bacterial taxa with 62 unique OTUs within families structing phylogenetic differences compared with only 18 taxa differentiating montane communities. Similar to bacteria and fungi, DOC and ammonium concentrations fluctuated predominantly by season while these same parameters where highly variable among urban soils among the three watersheds. Structural components of DOM via parallel factor analysis (PARAFAC) of fluorescence excitation-emission matrices show varying patterns between montane and urban systems with humic substance resistance to biodegradability found more dominantly in montane systems. Incorporating all soil chemical parameters, daily temperature and moisture, and fungal and bacterial diversity and richness in mixed linear effects models describing daily CO2 over all seasons, we found that a single model best described montane soil respiration, while individual watershed models best described urban respiration. Montane respiration was related to the availability of DOC, different DOM components, and rRNA-based bacterial diversity. Alternatively, urban respiration was influenced by either bacterial diversity and richness in our rapidly urbanizing environment, DOM characteristics and soil O2 in the more agricultural urban soils, or the DOM parameter humification index (HIX) in highly urbanized soils. Our results suggest that urbanization creates distinct bacterial and fungal communities with a single soil biotic or chemical parameter structuring soil respiration, while montane ecosystems select for similar bacterial and fungal communities with respiration sensitive to fluctuations in soil moisture, bacteria and the recalcitrance of carbon (C) resources.
Author: Haiying Sun
Publisher:
ISBN:
Category :
Languages : en
Pages : 282
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Author: Sharon Faye Smith
Publisher:
ISBN:
Category :
Languages : en
Pages : 348
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Soil microorganisms help maintain nutrient cycling, control carbon sequestration, impact plant productivity, and influence several soil chemical and physical properties; yet, the processes that control the microbial composition of soil and how environmental changes may affect the composition and activity of these organisms at different scales remains a difficult and intriguing puzzle for soil scientists, ecologists, and modelers. Wetlands are endangered and important ecosystems that provide several services, which are directly linked to soil function. However, few wetland assessments consider the soil environment and microbial ecology. Linking soil microbial community composition and distribution patterns to soil physio-chemical properties would provide fundamental information for the further exploration of how biogeochemical properties relate to ecosystem function, and pave the way towards developing new wetland success indicators. By using spatial ecology concepts along with soil metabarcoding, this research provides insight into the fungal and bacterial community composition and their relationship to the soil environment within a mounded wet prairie in southern United States. Generalized dissimilarity modeling (GDM), a form of nonlinear matrix regression, and amplicon metabarcoding was applied to simultaneously quantify the relative effects of geographic distance, elevation, and soil properties driving microbial community composition. The wet prairie surveyed in this research contained high spatial heterogeneity of soil chemical and physical properties, as well as distinct microtopography, which influenced the composition and diversity of soil microbial communities. The GDMs explained 28.3 and 41.5% of the total variation in bacterial and fungal beta diversity, respectively. Soil texture was an important and unexpected driver of both fungal and bacterial composition and diversity within the study site. Bacterial alpha diversity increased and fungal alpha diversity decreased with increasing sand content within the site. Sand content was also greatest on mounds in the site. Future wetland restoration studies should consider the influence of spatial heterogeneity of soil texture and micro-topography on microbial diversity, as it may affect the success of future restoration efforts. Understanding how soil microbial ecology connects to the soil environment at an ecosystem level can help inform future restoration practices, and can also be used to improve our predictive capabilities on a global scale for ecosystem services like carbon sequestration. The future applications of soil metagenomic data to infer ecosystem function and predict responses to a changing world are promising, but there are still many hurtles to overcome. While sequence databases are continuously growing, many metagenomic sequences still can't be aligned or assigned to a functional pathway. Thus, our ability to use metagenomic data for ecological models or to predict soil microbial response to climate change is dependent on continued efforts to characterize microbes and their associated environments.
Author: Samuel Evan Barnett
Publisher:
ISBN:
Category :
Languages : en
Pages : 0
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Soil dwelling microorganisms are essential components of numerous ecosystem processes and biogeochemical cycles. In particular, they are important actors in terrestrial carbon cycling, producing and turning over soil organic matter. Microbially mediated soil carbon cycling can be influenced by environmental conditions, with soil organic matter dynamics and carbon fate varying across biomes. Drastic alterations to soil habitat conditions brought about through anthropogenic changes to land-use (e.g. agriculture) can greatly influence these processes. However, we are limited in our understanding of how land-use regimes and other environmental conditions control microbially mediated soil carbon cycling. I took three approaches to explore this relationship. First, I examined how bacterial community assembly and composition differed across cropland, old-field, and forest soils. I found that homogeneous selection, whereby selection pressure causes bacterial communities to be more phylogenetically similar to each other than expected by random assembly from a metacommunity, was the dominant bacterial community assembly process across all three land-use types. However, I also found that land-use interacted with soil pH to drive the balance between stochastic and deterministic assembly processes. This result indicates a mechanism by which microbial communities may develop differently across land-use regimes. Second, I examined the overall organic matter turnover across land-use regimes and the identity of the bacterial taxa actively involved in this carbon processing. I found that the dynamics of organic matter turnover and the active bacterial populations involved were distinct across land-use regimes. From these patterns I developed a conceptual model explaining how initial microbial biomass, which is impacted by land-use, may control bacterial activities in organic matter turnover. Finally, I examined the genomic basis of bacterial life history strategies, specifically the copiotroph-oligotroph continuum. Life history strategy can explain both bacterial activity in soil carbon cycling and bacterial response to environmental change. I found that the abundance of transcription factor genes and genes encoding a secretion signal peptide were both genomic signatures of the copiotroph-oligotroph continuum. These signatures can be used to classify diverse microbes based on their life history strategy and may further explain the biological drivers of these strategies. I also developed a toolkit, MetaSIPSim, that simulates metagenomic DNA-stable isotope probing datasets. Such datasets can be used to improve metagenomic DNA-stable isotope probing methodologies and analyses, which in turn can be used to link microbial genes and genomes to in situ carbon cycling activity. Overall, this work advances our knowledge of, and ability to study the ecological and biological controls of bacterially mediated soil carbon cycling.
Author: Ru Li
Publisher:
ISBN:
Category :
Languages : en
Pages : 0
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Rhizosphere and soil bacteria are important drivers in nearly all biochemical cycles in terrestrial ecosystems and participate in maintaining health and productivity of soil in agriculturally managed systems. However, the effect of agricultural management systems on bacterial communities is still poorly understood. In this study, cultural methods and advanced molecular methods (terminal restriction fragment length polymorphism (TRFLP) and 454- pyrosequencing) were used to identify shifts in soil and rhizosphere bacterial diversity, community composition, and functions under different cropping systems in Manitoba, Canada. This included monoculture vs. rotation, zero tillage vs. conventional tillage, and organic farming vs. conventional farming. Results showed that: (1) different cropping systems did not significantly influence the diversity of bacterial communities. However, a significant variation in relative abundances of bacterial communities at both the phylum and genus level was observed among different cropping systems. Compared to conventional farming systems, organic farming system had a higher percentage of the phylum Proteobacteria (many Plant Growth Promoting Rhizosbacteria) and a lower percentage of the phylum Actinobacteria. When canola monoculture was compared to wheat-oat-canola-pea rotation, a significantly higher percentage of Proteobacteria and a lower percentage of Actinobacteria were found in the rotational system. Wheat monoculture shared similar bacterial communities with wheat-oat-canola-pea rotation. Zero tillage did not change bacterial community profiles except for an increase in Firmicutes (many PGPR), compared to conventional tillage. At the genus level, significant differences were found for the dominant genera Pseudomonas, Rhizobium, Stenotrophomonas, Brevundimonas, Burkholderia, Marmoricola, Microlunatus, and Solirubrobacter. The bacterial distribution was strongly associated with soil pH. (2) The cropping systems also influenced the antibiotic-producing Pseudomonas populations determined through PCR-based screening for the detection of genes involved in the biosynthesis of antibiotics. It was found that pyrrolnitrin- and phenazine- producing Pseudomonas spp. were more prevalent in the soil under zero tillage and organic farming systems, while 2,4-DAPG and pyoluteorin-producing strains were not found in this study. This comprehensive study provided fundamental information on how different cropping systems affect soil and rhizosphere bacterial communities, which can be used to guide Manitoba farmers to choose proper farming systems to maintain soil health and increase PGPR populations in soil.
Author:
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Languages : de
Pages :
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Bacteria are key players in nutrient cycles and energy transduction in soil. Although soil bacterial communities have been studied for several decades, our knowledge on their structure, dynamics ecosystem function is still limited. The aim of this thesis was to contribute to the understanding of these communities. In the first two studies, the impact of fertilizer treatment, two distinct aspen demes, soil properties (pH, water content, and C/N ratio), and sampling time on the total (DNA level) and the metabolic active (RNA level) bacterial community was analyzed. Thus, soil samples were col...
