Relationships Between Microbial Community Structure and Soil Processes Under Elevated Atmospheric Carbon Dioxide

There is little current understanding of the relationship between soil microbial community composition and soil processes rates, nor of the effect climate change and elevated CO₂ will have on microbial communities and their functioning. Using the eastern cottonwood (Populus deltoides) plantation at the Biosphere 2 Laboratory, we studied the relationships between microbial community structure and process rates, and the effects of elevated atmospheric CO₂ on microbial biomass, activity, and community structure. Soils were sampled from three treatments (400, 800, and 1200 ppm CO₂), a variety of microbial biomass and activity parameters were measured, and the bacterial community was described by 16S rRNA libraries. Glucose substrate-induced respiration (SIR) was significantly higher in the 1200 ppm CO₂ treatment. There were also a variety of complex, nonlinear responses to elevated CO₂. There was no consistent effect of elevated CO₂ on bacterial diversity; however, there was extensive variation in microbial community structure within the plantation. The southern ends of the 800 and 1200 ppm CO₂ bays were dominated by β-Proteobacteria, and had higher fungal biomass, whereas the other areas contained more α-Proteobacteria and Acidobacteria. A number of soil process rates, including salicylate, glutamate, and glycine substrate-induced respiration and proteolysis, were significantly related to the relative abundance of the three most frequent bacterial taxa, and to fungal biomass. Overall, variation in microbial activity was better explained by microbial community composition than by CO₂ treatment. However, the altered diversity and activity in the southern bays of the two high CO₂ treatments could indicate an interaction between CO₂ and light.     

Comparative Metagenomic Analysis of Soil Microbial Communities across Three Hexachlorocyclohexane Contamination Levels

This paper presents the characterization of the microbial community responsible for the in-situ bioremediation of hexachlorocyclohexane (HCH). Microbial community structure and function was analyzed using 16S rRNA amplicon and shotgun metagenomic sequencing methods for three sets of soil samples. The three samples were collected from a HCH-dumpsite (450 mg HCH/g soil) and comprised of a HCH/soil ratio of 0.45, 0.0007, and 0.00003, respectively. Certain bacterial; (Chromohalobacter, Marinimicrobium, Idiomarina, Salinosphaera, Halomonas, Sphingopyxis, Novosphingobium, Sphingomonas and Pseudomonas), archaeal; (Halobacterium, Haloarcula and Halorhabdus) and fungal (Fusarium) genera were found to be more abundant in the soil sample from the HCH-dumpsite. Consistent with the phylogenetic shift, the dumpsite also exhibited a relatively higher abundance of genes coding for chemotaxis/motility, chloroaromatic and HCH degradation (lin genes). Reassembly of a draft pangenome of Chromohalobacter salaxigenes sp. (∼8X coverage) and 3 plasmids (pISP3, pISP4 and pLB1; 13X coverage) containing lin genes/clusters also provides an evidence for the horizontal transfer of HCH catabolism genes.     

Transformation of Microbial Complexes in Components of Soil Constructions of Different Origin (Soil,Peat, Sand) during Freezing-thawing Processes

Microbiology - In a model experiment, the transformation of microbial complexes of cultivated saprotrophic bacteria and yeasts during freezing-thawing was studied in various natural substrates that...     

The Impact of Gamma Radiation on Sediment Microbial Processes

Microbial communities have the potential to control the biogeochemical fate of some radionuclides in contaminated land scenarios or in the vicinity of a geological repository for radioactive waste. However, there have been few studies of ionizing radiation effects on microbial communities in sediment systems. Here, acetate and lactate amended sediment microcosms irradiated with gamma radiation at 0.5 or 30 Gy h⁻¹ for 8 weeks all displayed NO₃⁻ and Fe(III) reduction, although the rate of Fe(III) reduction was decreased in 30-Gy h⁻¹ treatments. These systems were dominated by fermentation processes. Pyrosequencing indicated that the 30-Gy h⁻¹ treatment resulted in a community dominated by two Clostridial species. In systems containing no added electron donor, irradiation at either dose rate did not restrict NO₃⁻, Fe(III), or SO₄²⁻ reduction. Rather, Fe(III) reduction was stimulated in the 0.5-Gy h⁻¹-treated systems. In irradiated systems, there was a relative increase in the proportion of bacteria capable of Fe(III) reduction, with Geothrix fermentans and Geobacter sp. identified in the 0.5-Gy h⁻¹ and 30-Gy h⁻¹ treatments, respectively. These results indicate that biogeochemical processes will likely not be restricted by dose rates in such environments, and electron accepting processes may even be stimulated by radiation.     

Water Organic Pollution and Eutrophication Influence Soil Microbial Processes,Increasing Soil Respiration of Estuarine Wetlands: Site Study in Jiuduansha Wetland

Undisturbed natural wetlands are important carbon sinks due to their low soil respiration. When compared with inland alpine wetlands, estuarine wetlands in densely populated areas are subjected to great pressure associated with environmental pollution. However, the effects of water pollution and eutrophication on soil respiration of estuarine and their mechanism have still not been thoroughly investigated. In this study, two representative zones of a tidal wetland located in the upstream and downstream were investigated to determine the effects of water organic pollution and eutrophication on soil respiration of estuarine wetlands and its mechanism. The results showed that eutrophication, which is a result of there being an excess of nutrients including nitrogen and phosphorus, and organic pollutants in the water near Shang shoal located upstream were higher than in downstream Xia shoal. Due to the absorption and interception function of shoals, there to be more nitrogen, phosphorus and organic matter in Shang shoal soil than in Xia shoal. Abundant nitrogen, phosphorus and organic carbon input to soil of Shang shoal promoted reproduction and growth of some highly heterotrophic metabolic microorganisms such as β-Proteobacteria, γ-Proteobacteria and Acidobacteria which is not conducive to carbon sequestration. These results imply that the performance of pollutant interception and purification function of estuarine wetlands may weaken their carbon sequestration function to some extent.     

Impact of Fumigants on Soil Microbial Communities

Agricultural soils are typically fumigated to provide effective control of nematodes, soilborne pathogens, and weeds in preparation for planting of high-value cash crops. The ability of soil microbial communities to recover after treatment with fumigants was examined using culture-dependent (Biolog) and culture-independent (phospholipid fatty acid [PLFA] analysis and denaturing gradient gel electrophoresis [DGGE] of 16S ribosomal DNA [rDNA] fragments amplified directly from soil DNA) approaches. Changes in soil microbial community structure were examined in a microcosm experiment following the application of methyl bromide (MeBr), methyl isothiocyanate, 1,3-dichloropropene (1,3-D), and chloropicrin. Variations among Biolog fingerprints showed that the effect of MeBr on heterotrophic microbial activities was most severe in the first week and that thereafter the effects of MeBr and the other fumigants were expressed at much lower levels. The results of PLFA analysis demonstrated a community shift in all treatments to a community dominated by gram-positive bacterial biomass. Different 16S rDNA profiles from fumigated soils were quantified by analyzing the DGGE band patterns. The Shannon-Weaver index of diversity, H, was calculated for each fumigated soil sample. High diversity indices were maintained between the control soil and the fumigant-treated soils, except for MeBr (H decreased from 1.14 to 0.13). After 12 weeks of incubation, H increased to 0.73 in the MeBr-treated samples. Sequence analysis of clones generated from unique bands showed the presence of taxonomically unique clones that had emerged from the MeBr-treated samples and were dominated by clones closely related to Bacillus spp. and Heliothrix oregonensis. Variations in the data were much higher in the Biolog assay than in the PLFA and DGGE assays, suggesting a high sensitivity of PLFA analysis and DGGE in monitoring the effects of fumigants on soil community composition and structure. Our results indicate that MeBr has the greatest impact on soil microbial communities and that 1,3-D has the least impact.     

Patterns and Processes of Microbial Community Assembly

SUMMARY

Recent research has expanded our understanding of microbial community assembly. However, the field of community ecology is inaccessible to many microbial ecologists because of inconsistent and often confusing terminology as well as unnecessarily polarizing debates. Thus, we review recent literature on microbial community assembly, using the framework of Vellend (Q. Rev. Biol. 85:183–206, 2010) in an effort to synthesize and unify these contributions. We begin by discussing patterns in microbial biogeography and then describe four basic processes (diversification, dispersal, selection, and drift) that contribute to community assembly. We also discuss different combinations of these processes and where and when they may be most important for shaping microbial communities. The spatial and temporal scales of microbial community assembly are also discussed in relation to assembly processes. Throughout this review paper, we highlight differences between microbes and macroorganisms and generate hypotheses describing how these differences may be important for community assembly. We end by discussing the implications of microbial assembly processes for ecosystem function and biodiversity.     

The Temperature Sensitivity of the Processes of the Initial Stage of Microbial Decomposition of Woody Litter in Forest Soil

Biophysics - Abstract—Soil organic matter of forest ecosystems is characterized by high sensitivity to increased temperatures, which makes soil organic matter more vulnerable under the...     

Soil Microbial Community Responses to a Decade of Warming as Revealed by Comparative Metagenomics

Soil microbial communities are extremely complex, being composed of thousands of low-abundance species (<0.1% of total). How such complex communities respond to natural or human-induced fluctuations, including major perturbations such as global climate change, remains poorly understood, severely limiting our predictive ability for soil ecosystem functioning and resilience. In this study, we compared 12 whole-community shotgun metagenomic data sets from a grassland soil in the Midwestern United States, half representing soil that had undergone infrared warming by 2°C for 10 years, which simulated the effects of climate change, and the other half representing the adjacent soil that received no warming and thus, served as controls. Our analyses revealed that the heated communities showed significant shifts in composition and predicted metabolism, and these shifts were community wide as opposed to being attributable to a few taxa. Key metabolic pathways related to carbon turnover, such as cellulose degradation (∼13%) and CO₂ production (∼10%), and to nitrogen cycling, including denitrification (∼12%), were enriched under warming, which was consistent with independent physicochemical measurements. These community shifts were interlinked, in part, with higher primary productivity of the aboveground plant communities stimulated by warming, revealing that most of the additional, plant-derived soil carbon was likely respired by microbial activity. Warming also enriched for a higher abundance of sporulation genes and genomes with higher G+C content. Collectively, our results indicate that microbial communities of temperate grassland soils play important roles in mediating feedback responses to climate change and advance the understanding of the molecular mechanisms of community adaptation to environmental perturbations.     

Changes in the Fine Structure of Microbial Cells Induced by Chaotropic Salts

The electron microscopic examination of thin sections of cells of the yeasts Saccharomyces cerevisiae and Pichia pastoris and the gram-positive bacteria Micrococcus luteus and Bacillus subtilis showed that cell treatment with the chaotropic salts guanidine hydrochloride (6 M) and guanidine thiocyanate (4 M) at 37°C for 3–5 h or at 100°C for 5–6 min induced degradative processes, which affected almost all cellular structures. The cell wall, however, retained its ultrastructure, integrity, and rigidity, due to which the morphology of cells treated with the chaotropic salts did not change. High-molecular-weight DNA was localized in a new cell compartment, the ectoplasm (a peripheral hydrophilic zone). The chaotropic salts destroyed the outer and inner membranes and partially degraded the outer and inner protein coats of Bacillus subtilis spores, leaving their cortex (the murein layer) unchanged. The spore core became accessible to stains and showed the presence of regions with high and low electron densities. The conditions of cell treatment with the chaotropic salts were chosen to provide for efficient in situ PCR analysis of the 16S and 18S rRNA genes with the use of oligonucleotide primers.     

Rhizosphere Microbial Characterization in Petroleum-Contaminated Soil

Contamination of soil with petroleum compounds is of concern worldwide. Although there are a variety of physical and chemical technologies available to remediate petroleum waste sites, biological methods are often used due to lower cost and public acceptance. Growth and enhanced activity of microbial communities in contaminated soil is a key factor for the success of bioremediation. Establishing vegetation in petroleum-contaminated soil may enhance microbial activity and remediation success even further by providing root exudates to the rhizosphere microorganisms. In this study, microorganisms were characterized in petroleum-contaminated soils and sediments quantitatively and qualitatively based on enumeration and metabolic diversity assessments. Contaminated soils and sediments were obtained from a phytoremediation field demonstration project in California. Microbial numbers in the unvegetated soil, based on plate counts and most probable number of hydrocarbon degraders, were significantly lower than the vegetated soils. Metabolic microbial characterization using BIOLOG was also conducted and based on principle component analysis (PCA), there was a distinct difference between the metabolic diversity of microbial communities in vegetated and unvegetated soils. Results from this research indicate that the presence and type of plants, and level of contamination may greatly influence microbial communities in polluted soils.     

Optimization and Control of Industrial Microbial Cultivation Processes

Compared to the immense achievements in fundamental molecular biological sciences, the improvements in the fermentation and downstream processing technologies used in industry have been less spectacular over the last decade. Hence, there is a misbalance between new cellular systems and production technologies, resulting in a decreasing annual rate of approved production processes. In its PAT initiative the U.S. Food and Drug Administration identifies the potential for continuous improvement and makes concrete suggestions how this can be achieved. Here, some of these suggestions were applied to recombinant protein production with Escherichia coli and Pichia pastoris cultures. Concretely, the development of process operational procedures is discussed that allow a more tight supervision of the processes and the automatic control in cases where processes deviate from their set‐point profiles.     

Microbial Nitrogen Cycling Processes in a Sulfidic Coastal Marsh

Sulfide distribution is a key controller of vegetation zonation in coastal ecosystems, but data are limited regarding its impact on the spatial distribution of important N cycling processes. We assessed vegetation distribution and density and, mineral N pool sizes, composition and transformations in a sulfidic coastal marsh in relation to distance from sulfur springs. We observed strong relationships between vegetation attributes (species and density) and mineral N status with greater total inorganic N, NO₃⁻ and denitrification enzyme activity (DEA) in sediment samples from areas populated by Crithmum maritimum (mid-way between S springs and sea shore) than in sediments from areas colonized by either Agropyron repens (closest to the S springs) or mangrove (Rhizophora mangleL., farthest from the springs). Our data also suggest close links between N cycling and SO₄⁻² reduction. The latter resulted in net release of NH₄⁺ ranging from 0.9 mg N kg⁻¹ in the low density C. maritimum to 3.2 mg N kg⁻¹ in the high-density A. repens, during a 3-day incubation. We also tested for microbial adaptation to long-term high sulfide exposure by measuring DEA using the C₂H₂ block method (which has been found to be strongly affected by the presence of sulfide) and amendment of marsh sediment samples with NaMoO₄ to suppress reduced S production. In sediments extracted from sites near the sulfur springs (A. repens and C. maritimum), the C₂H₂ blockage assay yielded similar results without and with NaMoO₄ addition. However, in samples from a mangrove located further downstream from the springs, DEA was substantially lower (2.3 vs. 6.8 mg N₂O-N kg⁻¹ sediment d⁻¹) when production of reduced S was not inhibited by NaMoO₄. These results suggest that denitrifying microbes in the high sulfide areas may have adapted to the presence of sulfide, allowing for high rates of N and S cycling to occur simultaneously in these marshes.     

Geochemical Influence on Diversity and Microbial Processes in High Temperature Oil Reservoirs

The diversity of thermophilic microbial assemblages detected within two neighboring high temperature petroleum formations was shown to closely parallel the different geochemical regimes existing in each. A high percentage of archaeal 16S rRNA gene sequences, related to thermophilic aceticlastic and hydrogenotrophic methanogens, were detected in the natural gas producing Rincon Formation. In contrast, rRNA gene libraries from the highly sulfidogenic Monterey Formation contained primarily sulfur-utilizing and fermentative archaea and bacteria. In addition to the variations in microbial community structure, microbial activities measured in microcosm experiments using high temperature production fluids from oil-bearing formations also demonstrated fundamental differences in the terminal respiratory and redox processes. Provided with the same suite of basic energy substrates, production fluids from the South Elwood Rincon Formation actively generated methane, while thermophilic microflora within the Monterey production fluids were dominated by hydrogen sulfide producing microorganisms. In both cases, molecular hydrogen appeared to play a central role in the stimulation of carbon and sulfur cycling in these systems. In methanogenic production fluids, the addition of sulfur compounds induced a rapid shift in the terminal electron accepting process, stimulating hydrogen sulfide formation and illustrating the metabolic versatility of the subsurface thermophilic assemblage. The high similarity between microbial community structure and activity corresponding with the prevalent geochemical conditions observed in deep subsurface petroleum reservoirs suggests that the resident microflora have adapted to the subsurface physicochemical conditions and may actively influence the geochemical environment in situ.     

Effect of Four Organophosphorus Insecticides on Microbial Activities in Soil

Laboratory tests were conducted with four organophosphorus insecticides, Bay 37289 (O-ethyl O-2,4,5-trichlorophenyl ethylphosphonothioate), diazinon [O,O-diethyl O-(2-isopropyl-4-methyl-6-pyrimidinyl) phosphorothioate], Dursban (O,O-diethyl O-3,5,6-trichloro-2-pyridyl phosphorothioate), and Zinophos (O,O-diethyl O-2-pyrazinyl phosphorothioate), applied to a sandy loam at rates of 10 and 100 mug/g to determine whether these materials caused any serious effects on microbial activities related to soil fertility. All insecticides showed an effect on fungi and bacteria for the first and second week of incubation, but, subsequently, the populations returned to levels similar to those obtained in the controls. All insecticide applications increased ammonium production, but, in some instances, there appeared to be a slight depression of nitrification. Sulfur oxidation was equal to or better than that obtained with untreated soil in most cases. There was no significant effect on phosphorus mineralization. Oxygen consumption indicated that microbial respiration increased in proportion to the concentration of insecticides, suggesting the possibilities of microbial degradation of the insecticides or their degradation products and of uncoupling oxidative phosphorylation.     

养分管理对农田土壤微生物量的影响

土壤微生物与土壤质量、健康、植物的生产力和农业的可持续发展密切相关。任何对土壤中微生物的扰动都可能影响土壤的长期生产力,并可能产生严重后果。大量研究结果表明,肥料类型、施肥处理年限长短、施肥水平高低及施肥措施都会造成土壤成分的变化,进而影响土壤中微生物的生长以及繁殖。简要介绍了微生物量的几种测定方法,综述了各种养分管理措施对农田生态系统中土壤微生物量的影响,从而了解土壤微生物因人类对土壤的利用而发生的变化,以期为农业的可持续发展和生态环境的保护提供理论依据。     

Long-Term Explosive Contamination in Soil: Effects on Soil Microbial Community and Bioremediation

Explosive contamination in soil is a great concern for environmental health. Following 50 years of munitions manufacturing and loading, soils from two different sites contained ≥ 6,435 mg 2,4,6-trinitrotoluene (TNT), 2,933 mg hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) and 2,135 mg octahydrol-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) kg^{? 1} soil. Extractable nitrate-N was as high as 315 and ammonium-N reached 150 mg N kg^{? 1} soil. Water leachates in the highly contaminated soils showed near saturation levels of TNT and RDX, suggesting great risk to water quality. The long-term contamination resulted in undetectable fungal populations and as low as 180 bacterial colony forming units (CFU) g^–1 soil. In the most severely contaminated soil, dehydrogenase activity was undetectable and microbial biomass carbon was very low (< 3.4 mg C _mic kg^–1 soil). The diminished biological activity was a consequence of long-term contamination because short-term (14 d) contamination of TNT at up to 5000 mg TNT kg^–1 soil did not cause a decline in the culturable bacterial population. Natural attenuation may not be a feasible remediation strategy in soils with long-term contamination by high concentrations of explosives.     

Pyrene and Phenanthrene Influence on Soil Microbial Populations

Two studies were conducted to evaluate microbial populations in polycyclic aromatic hydrocarbon-contaminated soil. Captina silt loam was freshly exposed to (1) 0 or 2000?mg pyrene/kg and sampled after 10- and 61-wk incubation and (2) 0 or 505?mg pyrene + 445?mg phenanthrene/kg and sampled after a 21-wk incubation. Microbial numbers were determined by plate-count techniques. Isolated bacteria, selected degraders, and wholesoil extracts were analyzed by fatty acid methyl ester analysis (FAME). In the pyrene experiment, pyrene did not affect total bacterial or fungal numbers, but pyrene degraders increased from undetectable levels to 7.09 log₁₀ degraders/g in the contaminated soil. The FAME analysis of bacterial isolates detected no pyrene effect, but wholesoil FAME indicated an increase in the contaminated soil of a fatty acid characteristic of protozoa and a major fatty acid detected in isolated degraders. In the pyrene + phenanthrene experiment, the contaminants had no impact on bacterial, fungal, or actinomycete numbers but increased degrader numbers. No effect of pyrene + phenanthrene was detected by isolate FAME, but whole-soil FAME indicated an effect similar to that in the pyrene experiment. The results indicate that pyrene, although not impacting microbial numbers, may have altered the soil microbial composition and that Captina silt loam can develop an effective degrader population under tested conditions.